Managing the world’s freshwater supply to meet societal and environmental needs in a changing climate is one of the biggest challenges for the 21st century. Dams provide water security; however, the allocation of dwindling water supply among reservoirs could exacerbate or ameliorate the effects of climate change on aquatic communities. Here, we show that the relative sensitivity of river thermal regimes to direct impacts of climate change and societal decisions concerning water storage vary substantially throughout a river basin. In the absence of interspecific interactions, future Colorado River temperatures would appear to benefit both endemic and nonnative fish species. However, endemic species are already declining or extirpated in locations where their ranges overlap with warmwater nonnatives and changes in water storage may lead to warming in some of the coolest portions of the river basin, facilitating further nonnative expansion. Integrating environmental considerations into ongoing water storage negotiations may lead to better resource outcomes than mitigating nonnative species impacts after the fact.

Human activities create threats that have consequences for freshwater ecosystems and, in most watersheds, observed ecological responses are the result of complex interactions among multiple threats and their associated ecological alterations. Here we discuss the value of considering multiple threats in research and management, offer suggestions for filling knowledge gaps, and provide guidance for addressing the urgent management challenges posed by multiple threats in freshwater ecosystems. There is a growing literature assessing responses to multiple alterations, and we build off this background to identify three areas that require greater attention: linking observed alterations to threats, understanding when and where threats overlap, and choosing metrics that best quantify the effects of multiple threats. Advancing science in these areas will help us understand existing ecosystem conditions and predict future risk from multiple threats. Because addressing the complex issues and novel ecosystems that arise from the interaction of multiple threats in freshwater ecosystems represents a significant management challenge, and the risks of management failure include loss of biodiversity, ecological goods, and ecosystem services, we also identify actions that could improve decision-making and management outcomes. These actions include drawing insights from management of individual threats, using threat attributes (e.g., causes and spatio-temporal dynamics) to identify suitable management approaches, testing management strategies that are likely to be successful despite uncertainties about the nature of interactions among threats, avoiding unintended consequences, and maximizing conservation benefits. We also acknowledge the broadly applicable challenges of decision-making within a socio-political and economic framework, and suggest that multidisciplinary teams will be needed to innovate solutions to meet the current and future challenge of interacting threats in freshwater ecosystems.

Lay Abstract Air–water gas exchange governs the rate at which atmospheric gases flow into and out of aquatic ecosystems. Knowing this rate is necessary to calculate river photosynthesis and respiration, but there are few data from large rivers, and there are no data that include whitewater rapids. We studied the Colorado River, Grand Canyon; this river has flat reaches separated by extremely large, steep, whitewater rapids. We measured gas transfer velocity (the height of the water column that can exchange all of its gas per hour) by measuring how quickly the river gained oxygen as it flowed over the first 7 major rapids. The Colorado River has low oxygen concentration as it flows out of Glen Canyon Dam, located 25 kilometers upriver from Lees Ferry. We found that gas transfer velocity increased as river slope increased. Gas transfer velocity was low in flat reaches but was up to 800 times higher in rapids, which were the highest rates ever measured in a river. Based on the rate of change of oxygen concentration per meter of river drop, we estimated gas transfer velocity for the remainder of the Colorado River in Grand Canyon. Gas exchange varied 5‐fold depending on the slope of the immediate reach. Gas transfer velocity was higher for the Colorado River than for other aquatic ecosystems because of its large rapids. Our approach of scaling gas transfer velocity to the entire river will allow comparing gas transfer velocity across rivers that have variable river slopes, such as the Colorado River, Grand Canyon.