Nutrient effluents from urban and agricultural inputs have resulted in high concentrations of nitrate in freshwater ecosystems. Exposure to nitrate can be particularly threatening to aquatic organisms, but a quantitative synthesis of the overall effects on amphibians, amphipods and fish is currently unavailable. Moreover, in disturbed ecosystems, organisms are unlikely to face a single stressor in isolation, and interactions among environmental stressors can enhance the negative effects of nitrate on organisms. Here, the effects of elevated nitrate on activity level, deformity rates, hatching success, growth and survival of three taxonomic groups of aquatically respiring organisms are documented. Effect sizes were extracted from 68 studies and analysed using meta-analytical techniques. The influence of nitrate on life-stages was also assessed. A factorial meta-analysis was conducted to examine the effect of nitrate and its interaction with other ecological stressors on organismal survival. Overall, the impacts of nitrate are biased towards amphibians (46 studies) and fish (13 studies), and less is known about amphipods (five studies). We found that exposure to nitrate translates to a 79% decrease in activity, a 29% decrease in growth, and reduces survival by 62%. Nitrate exposure also increases developmental deformities but does not affect hatching success. Nitrate exposure was found to influence all life-stages except embryos. Differences in the sensitivity of nitrate among taxonomic groups tended to be negligible. The factorial meta-analysis (14 amphibians and two amphipod studies) showed that nitrate in combination with other stressors affects survival in a non-additive manner. Our results indicate that nitrate can have strong effects on aquatic organisms and can interact with other environmental stressors which compound the negative effects on survival. Overall, the impacts of nitrate and additional stressors are complex requiring a holistic approach to better conserve freshwater biodiversity in the face of ongoing global change.