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1.
  1. Limnological aspects of Amazon floodplain lakes are examined in the context of aquatic conservation.
  2. A prerequisite to detecting and evaluating changes that could threaten the ecological health and organisms in floodplain lakes is understanding variation under present conditions. Based on one of the few studies with regular measurements over 2 years, chlorophyll, total phosphorus, dissolved oxygen, transparency, and total suspended solids in Lake Janauacá indicate that the lake is naturally quite variable with a mesotrophic to eutrophic status.
  3. Direct threats to ecological health of floodplain lakes include mining operations that can increase turbidity and trace metals and reduce nutritional quality of sediments. Mercury contamination and methylation leads to bioaccumulation in aquatic organisms.
  4. Deforestation in uplands increases nitrogen and phosphorus inputs to floodplain lakes and can alter trophic status. Deforestation in floodable forests alters the habitat and food of the fish that inhabit these forests.
  5. Cumulative limnological responses as catchments are altered by urban, agricultural, and industrial developments, and as inundation is altered by changes in climate and construction of dams, have major implications for the ecology of floodplain lakes.
  6. To improve understanding and management of threats to the conservation of aquatic Amazon biota and ecosystems requires considerably expanded and coordinated research and community-based management that includes the spectrum of floodplain lakes throughout the basin.
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2.
  1. The Burdekin River floodplain wetlands are internationally important and act as a sink for sediments and nutrients that would otherwise enter the World Heritage‐listed Great Barrier Reef lagoon.
  2. The Burdekin River has the highest natural discharge of any Great Barrier Reef catchment and contributes the greatest mass of sediment to the reef. The river and its catchment have been substantially modified by land clearance, river regulation introduced in the 1960s, the construction of the Burdekin Falls Dam in 1987 and invasive aquatic plants.
  3. We hypothesised that the natural variability of Burdekin River discharge would render its wetland ecosystems resistant to human‐induced pressures.
  4. Diatoms were analysed from the sediments of two lower Burdekin River floodplain wetlands with contrasting regulation histories. Labatt Lagoon has a long history of flow alteration, whereas Swan's Lagoon has experienced limited regulation.
  5. Both wetlands experienced dramatic increases in sedimentation as a result of land clearance, yet the Swan's Lagoon diatom record indicates that the wetland's ecology remains within the range of natural variability. In contrast, Labatt Lagoon is markedly different from its pre‐settlement state. It is now permanent, having been ephemeral for more than 1000 years before European settlement. The conversion to artificial permanence facilitated aquatic plant invasion, resulting in more marked changes than widespread pastoralism.
  6. Modern diatom assemblages from 28 lower Burdekin River floodplain wetlands indicate that the contemporary flora of Swan's Lagoon is unusual. Most wetlands have similar assemblages to those in the Labatt Lagoon record in its present, altered state. It is possible, therefore, that the ecological shift registered in Labatt Lagoon is widespread.
  7. Diatom records highlight the striking impact that river regulation has had on the trajectory of the Burdekin floodplain wetlands. It is likely that wetland rehabilitation can be facilitated by the re‐introduction of a variable hydrological regime.
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3.
  1. The extent and intensity of impacts of multiple new dams in the Amazon basin on specific biological groups are potentially large, but still uncertain and need to be better understood.
  2. It is known that river disruption and regulation by dams may affect sediment supplies, river channel migration, floodplain dynamics, and, as a major adverse consequence, are likely to decrease or even suppress ecological connectivity among populations of aquatic organisms and organisms dependent upon seasonally flooded environments.
  3. This article complements our previous results by assessing the relationships between dams, our Dam Environmental Vulnerability Index (DEVI), and the biotic environments threatened by the effects of dams. Because of the cartographic representation of DEVI, it is a useful tool to compare the potential hydrophysical impacts of proposed dams in the Amazon basin with the spatial distribution of biological diversity. As the impact of Amazonian dams on the biota of both rivers and periodically flooded riparian environments is severe, DEVIs from different Amazonian tributary basins are contrasted with patterns of diversity and distribution of fish, flooded forest trees and bird species.
  4. There is a consistent relationship between higher DEVI values and the patterns of higher species richness and endemism in all three biological groups. An assessment of vulnerability at the scale of tributary basins, the assessment of biodiversity patterns related to DEVI, and the analysis of teleconnections at basin scale, demonstrate that recent construction of dams is affecting the biota of the Amazon basin.
  5. The evidence presented here predicts that, if currently planned dams are built without considering the balance between energy production and environmental conservation, their cumulative effects will increase drastically and represent a major threat to Amazonian biodiversity.
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4.
  1. The Amazon basin has been subjected to extreme climatic events and according to climate change projections this hydrosystem could face changes in the natural dynamic of flood cycles that support the feeding and reproduction of many fish species, threatening aquatic biodiversity.
  2. Protected areas (PAs) are the main tools used to safeguard the biodiversity in the long term; however, they are fixed areas that could be subject to climate change, questioning their future efficiency in protecting biodiversity.
  3. The Amazon basin currently benefits from a relatively high level of protection as 52% of its catchment area is under the form of true PAs or indigenous lands. However, the capacity of these PAs to protect freshwater biodiversity remains unclear as they have generally been assessed with little regard to freshwater ecosystems and their hydrological connectivity. Here, the aim was to evaluate the effectiveness of PAs in representing the Amazon fish fauna under current and future climatic conditions.
  4. A macroecological approach was used to estimate the minimum size of the geographical range needed by each species to achieve long-term persistence, by a combined function of range size and body size, two ecological traits known to influence species extinction risk.
  5. In future the Amazon basin could risk losing 2% of its freshwater fish fauna owing to unsuitable climatic conditions, with a further 34% adversely affected. The present Amazon network of PAs will cover the minimum required range for species persistence for more than 60% of the freshwater fish species analysed under the future climate scenario. However, more than 25% of the future susceptible species are currently concentrated in large tributaries and in the central-lower Amazon floodplain where few PAs occur, highlighting the lack of appropriate conservation actions for these specific water bodies.
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5.
  1. The Balbina hydropower dam in the Central Amazon basin, established in the Uatumã River in the 1980s, is emblematic for its socio-environmental disaster. Its environmental impacts go far beyond the reservoir and dam, however, affecting the floodplain forests (igapó) in the downstream area (dam shadow), which have been assessed using a transdisciplinary research approach, synthesized in this review.
  2. Floodplain tree species are adapted to a regular and predictable flood pulse, with high- and low-water periods occurring during the year. This was severely affected by the operation of the Balbina dam, which caused the suppression of both the aquatic phase at higher floodplain elevations and the terrestrial phase at lower floodplain elevations (termed the ‘sandwich effect’).
  3. During the period of construction and reservoir fill, large-scale mortality already occurred in the floodplains of the dam shadow as a result of reduced stream flow, in synergy with severe drought conditions induced by El Niño events, causing hydraulic failure and making floodplains vulnerable to wildfires.
  4. During the operational period of the dam, permanent flooding conditions at low topographical elevations resulted in massive tree mortality. So far, 12% of the igapó forests have died along a downstream river stretch of more than 125 km. As a result of flood suppression at the highest elevations, an encroachment of secondary tree species from upland (terra firme) forests occurred.
  5. More than 35 years after the implementation of the Balbina dam, the downstream impacts caused massive losses of macrohabitats, ecosystem services, and diversity of flood-adapted tree species, probably cascading down to the entire food web, which must be considered in conservation management.
  6. These findings are discussed critically, emphasizing the urgent need for the Brazilian environmental regulatory agencies to incorporate downstream impacts in the environmental assessments of several dam projects planned for the Amazon region.
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6.
  1. Globally, river systems have been extensively modified through alterations in riverscapes and flow regimes, reducing their capacity to absorb geophysical and environmental changes.
  2. In western North America and elsewhere, alterations in natural flow regimes and swimways through dams, levees, and floodplain development, work in concert with fire regime, forest management practices, as well as agriculture and urban development, to change recovery trajectories of river systems.
  3. Hydroregime scenarios for coho salmon, Oncorhynchus kisutch (Walbaum, 1792), were investigated in Washington and Oregon, USA, where long‐term records of discharge, water temperature, and upstream fish passage are available. This novel approach combines hydrological and ecological data in a single visualization, providing empirical foundations for understanding upstream behavioural movement and tolerances of native fishes.
  4. The timing of coho salmon movement with respect to temperature and discharge were compared with scenarios representing possible future hydrological conditions associated with a changing climate.
  5. This approach provides a framework for the study of future hydrological alterations in other locations, and can inform local and regional conservation planning, particularly in view of water management policy. Management implications and recommendations for action that may expand the capacity of riverscapes to absorb perturbations are discussed.
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7.
  1. The ecosystem services provided by freshwater biodiversity are threatened by development and environmental and climate change in the Anthropocene.
  2. Here, case studies are described to show that a focus on the shared dependence on freshwater ecosystem functioning can mutually benefit fisheries and conservation agendas in the Anthropocene.
  3. Meeting the threat to fish biodiversity and fisher livelihood is pertinent in developing regions where there is often a convergence between high biodiversity, high dependency on aquatic biota and rapid economic development (see Kafue River, Logone floodplain, Tonle Sap, and Rio Negro case studies).
  4. These case studies serve as evidence that biodiversity conservation goals can be achieved by emphasizing a sustainable fisheries agenda with partnerships, shared knowledge and innovation in fisheries management (see Kafue River and Kenai River case studies).
  5. In all case studies, aquatic biodiversity conservation and fisheries agendas are better served if efforts focused on creating synergies between fishing activities with ecosystem functioning yield long‐term livelihood and food security narratives.
  6. A unified voice from conservation and fisheries communities has more socio‐economic and political capital to advocate for biodiversity and social interests in freshwater governance decisions.
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8.
  1. The Amazon Basin is being degraded at unprecedented rates, yet conservation efforts have implemented protected areas to curb deforestation, leaving freshwater ecosystems vulnerable to degradation. Amazon freshwater ecosystems are largely unprotected because a terrestrial bias has limited the ability of science to affect policy.
  2. Overcoming this bias requires increasing exchange of information among stakeholders across the basin to raise awareness of threats to Amazon freshwater ecosystems and promote discussions and access to conservation solutions. To help address this need, this Special Issue collates 15 synthetic articles that advance knowledge and identify conservation solutions.
  3. Three articles highlight the importance of considering the hydrological and limnological processes that control the integrity of these freshwater ecosystems and offer new insights on how to extrapolate them across the basin.
  4. Three articles on crocodilians, aquatic mammals, and migratory fishes document threats and knowledge gaps, and identify the missing role of governments as an impediment to conservation of their populations.
  5. Three articles evaluate the multi-faceted effects of hydropower dams on fish, birds, and floodplain trees. They reinforce perceptions that dams are key environmental threats and offer guidance for improving protocols for dam site selection and impact assessment.
  6. Three articles assessing the effectiveness of protected areas to safeguard fish and aquatic invertebrates show there is an urgent need to redesign the Amazon protected area network to adequately protect freshwater biota.
  7. Three forward-looking articles show that: (i) conservation initiatives by local communities are ‘bright spots’ for freshwater conservation; (ii) microchemistry analyses of the ear bones of fishes could boost the knowledge base needed to conserve them; and (iii) strengthening the Amazon conservation framework requires a reversal of Brazil's current governmental priorities, remobilization of stakeholders, investments in capacity building, and expanding protections to terrestrial and freshwater ecosystems.
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9.
  1. This study examined the assisted natural restoration of native vegetation in an Australian floodplain wetland where flows were reinstated and the river was reconnected to the floodplain, following cessation of agricultural cultivation.
  2. Extant vegetation was surveyed three times during an inundation event at plots with different land‐use histories.
  3. Restoration rate was more influenced by past land use than long‐term inundation frequency and success decreased with antecedent land‐use intensity. Prolonged land‐use history (>3 years cultivation) restricted restoration success. Sites with longer cultivation histories tended to have fewer aquatic species, more terrestrial species and exotic species. For example, amphibious responders with floating leaves were found only in reference plots and less frequently in farmed treatment plots. In this scenario, increased persistence of exotics and dryland species suggested alternative trajectories. Fields with a short land‐use history (1–3 years of clearing and cultivation) resembled undisturbed floodplain communities, consistent with a ‘field of dreams’ hypothesis.
  4. Although river–floodplain reconnections can restore wetlands, legacy effects of past land use may limit the pace and outcomes of restoration.
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10.
  1. The paper ‘Biodiversity values of remnant freshwater floodplain lagoons in agricultural catchments: evidence for fish of the Wet Tropics bioregion, northern Australia’, published in Aquatic Conservation: Marine and Freshwater Ecosystems in 2015, has contributed in several ways to the integration of freshwater wetland science within new catchment management policies and practices for Great Barrier Reef (GBR) sustainability.
  2. The Tully–Murray biodiversity study developed novel protocols to sample larval, juvenile, and adult fish life‐history stages in floodplain lagoons using a combination of boat‐based backpack electrofishing and fyke netting. In addition, hydrological and hydrodynamic models were applied in a completely new way to quantify the timing, extent, and duration of water connectivity across floodplain streams, cane drains, and wetlands. Combining the two novel approaches enabled an analysis of lagoon fish assemblage patterns in relation to environmental gradients, especially floodplain hydrology, connectivity patterns, and measures related to agricultural land use.
  3. In demonstrating the importance of different levels of connectivity for different biodiversity outcomes in freshwater floodplain lagoons of the Tully–Murray catchment, the subject paper established that floodplain connectivity needs to be taken into consideration in wetland management practices.
  4. The timing of the subject publication was fortuitous. It coincided with the preparation of the evidence‐based 2017 Scientific Consensus Statement on land‐based water quality impacts on the GBR. As one of the few freshwater wetland ecology publications for the catchments of the GBR at that time, this paper played an important role in demonstrating freshwater wetland values, fish conservation options, and management imperatives to sustain wetland ecological health and services in GBR catchments.
  5. By advancing the understanding of factors driving biodiversity patterns, and the importance of connectivity and ecohydrological processes in freshwater floodplain wetlands of the GBR catchment, the Tully–Murray study helped to drive new policy directives for the protection and restoration of catchment, floodplain, and estuary functions, and connectivity, now embedded in the Reef 2050 Long‐Term Sustainability Plan 2018, an overarching strategy for managing the GBR over the next 35 years, and complementary Queensland environmental legislation.
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11.
  1. Environmental water management seeks to balance competing demands between the water needed to sustain human populations and their economic activities and that required to sustain functioning freshwater ecosystems and the species they support. It must be predicated on an understanding of the environmental, hydrological, and biological factors that determine the distribution and abundance of aquatic species.
  2. The Daly River of the wet–dry tropics of northern Australia consists of a perennially flowing main stem and large tributaries, as well as many small to large naturally intermittent tributaries, and associated off‐channel wetlands. Increased groundwater abstraction to support irrigated agriculture during the dry season threatens to reduce dry‐season flows that maintain perenniality and persistence of freshwater fishes.
  3. Fish assemblages were surveyed at 55 locations during the dry season over a 2‐year period with the goal of establishing the key landscape‐scale and local‐scale (i.e. habitat) drivers of fish species distribution.
  4. Longitudinal (upstream/downstream) and lateral (river/floodplain) gradients in assemblage structure were observed with the latter dependent on the position in the river landscape. Underlying these gradients, stream flow intermittency influenced assemblage composition, species richness, and body size distributions. Natural constraints to dispersal were identified and their influence on assemblage structure was also dependent on position within the catchment.
  5. Eight distinct assemblage types were identified, defined by differences in the abundance of species within five groups differing in functional traits describing body size, spawning requirements, and dispersal capacity. These functional groups largely comprised species widely distributed in northern Australia.
  6. The results of the study are discussed with reference to the environmental flow needs of the Daly River and other rivers of northern Australia. The findings may also be applied to environmental flow management in savannah rivers elsewhere.
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12.
13.
  1. Juvenile Pacific salmon exhibit diverse habitat use and migration strategies to navigate high environmental variability and predation risk during freshwater residency. Increasingly, urbanization and climate-driven hydrological alterations are affecting the availability and quality of aquatic habitats in salmon catchments. Thus, conservation of freshwater habitat integrity has emerged as an important challenge in supporting salmon life-history diversity as a buffer against continuing ecosystem changes.
  2. To inform catchment management for salmon, information on the distribution and movement dynamics of juvenile fish throughout the annual seasonal cycle is needed. A number of studies have assessed the ecology of juvenile coho salmon (Oncorhynchus kisutch) during summer and autumn seasons; catchment use by this species throughout the annual cycle is less well characterized, particularly in high-latitude systems.
  3. Here, n = 3,792 tagged juvenile coho salmon were tracked throughout two complete annual cycles to assess basin-wide distribution and movement behaviour of this species in a subarctic, ice-bearing catchment.
  4. Juvenile coho salmon in the Big Lake basin, Alaska, exhibited multiple habitat use and movement strategies across seasons; however, summer rearing in lotic mainstem environments followed by migration to lentic overwinter habitats was identified as a prominent behaviour, with two-thirds of tracked fish migrating en masse to concentrate in a small subset of upper catchment lakes for the winter. In contrast, the most significant tributary overwintering site (8% of tracked fish) occurred below a culvert and dam, blocking juvenile fish passage to a headwater lake, indicating that these fish may have been restricted from reaching preferred lentic overwinter habitats.
  5. These findings emphasize the importance of maintaining aquatic connectivity to lentic habitats as a conservation priority for coho salmon during freshwater residency.
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14.
15.
  1. Changes in migration timing, resulting from the alteration in river continuity or the effect of climate change, can have major consequences on the population dynamics of diadromous fish. Forecasting the phenology of fish migration is thus critically important to implement management actions aimed at protecting fish during their migration.
  2. In this study, an 11‐year monitoring survey of Atlantic salmon smolts (Salmo salar) from the Ourthe River, Belgium, was analysed within a European Special Area of Conservation to improve the understanding of environment‐induced spring migration. A logistic model was fitted to forecast smolt migration and to calculate phenological indicators for management, i.e. the onset, end, and duration of migration, while accounting for the influence of photoperiod, water temperature, and hydrological conditions.
  3. The results indicated that the photo‐thermal units accumulated by smolts above a 7°C temperature threshold was a relevant proxy to reflect the synergistic effect between temperature and photoperiod on smolt migration. After integrating the effect of river flow pulses, the model accurately explained the inter‐annual changes in migration timing (R2 = 0.95). The model predictions provide decisive management information to identify sensitive periods during which mitigation measures (e.g. hydropower turbine shutdown, river discharge management) should be conducted to promote smolt survival.
  4. The model was used to predict phenological characteristics under future scenarios of climate change. The results suggest a joint effect of hydrological alterations and water warming. Temperature increases of 1–4°C were associated with earlier initiation of migration, 6–51 days earlier, and spring flood events greatly influenced the duration of the migration period. Accordingly, the combined effects of human‐induced modifications of the hydrological regimes and increasing temperatures could result in a mismatch between the smolt and favourable survival conditions in the marine environment.
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16.
  1. In many wetlands the timing and duration of inundation determine ecological characteristics and the provision of ecosystem services; however, wetland conservation decisions often rely on static maps of wetland boundaries that do not capture their dynamic hydrological variability and connectivity.
  2. The Amazon River basin contains some of the world's most extensive wetlands, many of which are floodplains where seasonal flood pulses result in a temporally varying inundation area and hydrological connectivity with river systems.
  3. This study classified Amazon wetlands according to the timing and duration (months per year) of inundation detected by remote sensing, and also investigated the contribution of precipitation regimes in affecting wetland distribution and hydrological dynamics.
  4. Permanently inundated wetlands account for the largest area and are mainly floodplains located in the lowlands of the catchment. Seasonally inundated wetlands varied greatly in the duration of inundation over the course of the year, ranging from 1 to 9 months. Distinct seasonal timing was detected among the large wetland complexes, reflecting rainfall regimes as well as time lags for drainage and drying. For example, inundation in the extensive Llanos de Moxos region of the southern Amazon was protracted and lasted well after the rainy season, compared with the Roraima region of the northern Amazon, where inundation was shorter and tracked the rainy season.
  5. The integration of inundation dynamics into wetland classification captures regional differences in timing and duration of inundation in the major wetlands of the basin that should be considered for conservation planning and other ecological applications. This information can aid regional wetland management and planning, especially with regards to minimizing the effects of dam and waterway construction that can directly affect the natural wetland dynamics. The use of global remotely sensed inundation data makes this approach easily transferable to other large tropical wetlands.
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17.
  1. Systematic conservation planning in freshwater ecosystems faces multiple challenges because of the dynamic nature of rivers and their multiple dimensions of connectivity. In intermittent hydrological systems connectivity is functional when water is available, allowing the exchange of aquatic individuals between isolated freshwater ecosystems. Integrating these isolated systems in their hydrological context is essential when identifying priority areas for conservation, in order to try to minimize the propagation of threats into target water bodies (management units) from the surrounding landscape.
  2. Here, the use of a systematic planning approach is demonstrated to identify a set of priority management units to preserve freshwater biodiversity in an arid system of fragmented water bodies immersed in a landscape subject to a range of impacts.
  3. Twenty-six water-dependent taxa from 59 mountain rock pools (gueltas) of three southern Mauritanian mountains were used as a case study. A conservation planning tool (marxan ) was used to find priority conservation areas to integrate intermittent hydrological systems in their hydrological context, promote connectivity, and minimize the downstream propagation of threats. Three types of connectivity were analysed: (i) no connectivity, (ii) connectivity between gueltas, and (iii) connectivity between gueltas and sub-catchments.
  4. Considering different types of longitudinal connectivity affects the number and spatial allocation of the priority gueltas selected, and the conservation status of the gueltas and their upstream areas. Incorporating connections between gueltas and upstream locations in the modelling resulted in the selection of gueltas in areas with a low human footprint and in the increased connectivity of the solutions.
  5. The results obtained revealed important locations for local biodiversity conservation, and the method presented can be used when assessing the propagation of potential waterborne threats into isolated management units. The framework developed allows connectivity to be addressed in conservation planning. It can be replicated in regions with similar isolated habitats that connect through intermittent hydrological systems and can also be applied to lateral and vertical hydrological connectivity.
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18.
19.
20.
  1. Today, aquatic biodiversity suffers from many pressures linked to human activities, including climate change, which particularly affects alpine areas. Many alpine freshwater species have shifted their geographical distribution to colder areas, but a reduced availability of suitable habitats is also forecasted. New artificial water bodies could provide habitat enhancement opportunities, including small mountain reservoirs built to overcome a lack of snow during winter.
  2. To investigate the role of reservoirs as a habitat for freshwater invertebrates, a case study was conducted on eight reservoirs in the Swiss Alps. The study aimed to compare the water quality and freshwater biodiversity of the reservoirs with those of 39 natural and newly excavated ponds. Data were collected on physico‐chemistry, freshwater habitat structure, and aquatic insects (dragonflies and aquatic beetles).
  3. The study showed that the mountain reservoirs investigated did not differ from natural ponds in terms of surface area, conductivity, and trophic level. Similarly to natural ponds, reservoirs showed signs of impairment owing to surface run‐off carrying pollutants linked to ski tourism. They presented a low diversity of mesohabitats, and in particular lacked vegetation. Compared with natural ponds, the species richness in reservoirs was lower for dragonflies but not for beetles. At the regional scale, the community from the reservoirs was a subset of the natural ponds community, supporting 38% of the regional species richness for these two insect groups.
  4. The results suggest that mountain reservoirs are likely to be important for biodiversity in alpine areas, both as habitats and as stepping stones for species shifting their geographical range. These water bodies can be enhanced further by some nature‐friendly measures to maximize benefits for biodiversity, including margin revegetation or the creation of adjacent ponds. Ecological engineering needs to be innovative and promote freshwater biodiversity in artificial reservoirs.
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