In the 12 years since Dudgeon et al. (2006) reviewed major pressures on freshwater ecosystems, the biodiversity crisis in the world's lakes, reservoirs, rivers, streams and wetlands has deepened. While lakes, reservoirs and rivers cover only 2.3% of the Earth's surface, these ecosystems host at least 9.5% of the Earth's described animal species. Furthermore, using the World Wide Fund for Nature's Living Planet Index, freshwater population declines (83% between 1970 and 2014) continue to outpace contemporaneous declines in marine or terrestrial systems. The Anthropocene has brought multiple new and varied threats that disproportionately impact freshwater systems. We document 12 emerging threats to freshwater biodiversity that are either entirely new since 2006 or have since intensified: (i) changing climates; (ii) e-commerce and invasions; (iii) infectious diseases; (iv) harmful algal blooms; (v) expanding hydropower; (vi) emerging contaminants; (vii) engineered nanomaterials; (viii) microplastic pollution; (ix) light and noise; (x) freshwater salinisation; (xi) declining calcium; and (xii) cumulative stressors. Effects are evidenced for amphibians, fishes, invertebrates, microbes, plants, turtles and waterbirds, with potential for ecosystem-level changes through bottom-up and top-down processes. In our highly uncertain future, the net effects of these threats raise serious concerns for freshwater ecosystems. However, we also highlight opportunities for conservation gains as a result of novel management tools (e.g. environmental flows, environmental DNA) and specific conservation-oriented actions (e.g. dam removal, habitat protection policies, managed relocation of species) that have been met with varying levels of success. Moving forward, we advocate hybrid approaches that manage fresh waters as crucial ecosystems for human life support as well as essential hotspots of biodiversity and ecological function. Efforts to reverse global trends in freshwater degradation now depend on bridging an immense gap between the aspirations of conservation biologists and the accelerating rate of species endangerment.

Climate change-induced increases in summer water temperature have been associated with elevated mortality of adult sockeye salmon (Oncorhynchus nerka) during river migration. We show that cardiorespiratory physiology varies at the population level among Fraser River sockeye salmon and relates to historical environmental conditions encountered while migrating. Fish from populations with more challenging migratory environments have greater aerobic scope, larger hearts, and better coronary supply. Furthermore, thermal optima for aerobic, cardiac, and heart rate scopes are consistent with the historic river temperature ranges for each population. This study suggests that physiological adaptation occurs at a very local scale, with population-specific thermal limits being set by physiological limitations in aerobic performance, possibly due to cardiac collapse at high temperatures.

Elevated river water temperature in the Fraser River, British Columbia, Canada, has been associated with enhanced mortality of adult sockeye salmon (Oncorhynchus nerka) during their upriver migration to spawning grounds. We undertook a study to assess the effects of elevated water temperatures on the gill transcriptome and blood plasma variables in wild-caught sockeye salmon. Naturally migrating sockeye salmon returning to the Fraser River were collected and held at ecologically relevant temperatures of 14°C and 19°C for seven days, a period representing a significant portion of their upstream migration. After seven days, sockeye salmon held at 19°C stimulated heat shock response genes as well as many genes associated with an immune response when compared with fish held at 14°C. Additionally, fish at 19°C had elevated plasma chloride and lactate, suggestive of a disturbance in osmoregulatory homeostasis and a stress response detectable in the blood plasma. Fish that died prematurely over the course of the holding study were compared with time-matched surviving fish; the former fish were characterized by an upregulation of several transcription factors associated with apoptosis and downregulation of genes involved in immune function and antioxidant activity. Ornithine decarboxylase (ODC1) was the most significantly upregulated gene in dying salmon, which suggests an association with cellular apoptosis. We hypothesize that the observed decrease in plasma ions and increases in plasma cortisol that occur in dying fish may be linked to the increase in ODC1. By highlighting these underlying physiological mechanisms, this study enhances our understanding of the processes involved in premature mortality and temperature stress in Pacific salmon during migration to spawning grounds.

Elevated river temperatures have been associated with high mortality in migrating adult sockeye salmon, which may be partially attributed to physiological limitations in aerobic performance. This study suggests that the decrease in aerobic scope above optimum temperatures is due to a cardiac limitation, triggered by reduced scope for heart rate.

Global climate change is altering freshwater ecosystems and affecting fish populations and communities. Underpinning changes in fish distribution and assemblage‐level responses to climate change are individual‐level physiological constraints. In this review, we synthesize the mechanistic effects of climate change on neuroendocrine, cardiorespiratory, immune, osmoregulatory, and reproductive systems of freshwater and diadromous fishes. Observed climate change effects on physiological systems are varied and numerous, including exceedance of critical thermal tolerances, decreased cardiorespiratory performance, compromised immune function, and altered patterns of individual reproductive investment. However, effects vary widely among and within species because of species, population, and even sex‐specific differences in sensitivity and resilience and because of habitat‐specific variation in the magnitude of climate‐related environmental change. Research on the interactive effects of climate change with other environmental stressors across a broader range of fish diversity is needed to further our understanding of climate change effects on fish physiology.