Aquatic animals are a key component of streams and lakes biogeochemistry as these release nutrients and carbon via their excretion. Animal nutrient excretion may vary with animal taxonomic rank, trophic position and abiotic factors such as light and nutrient supply. Light and nutrient supply is modulated by dissolved organic matter (DOM) which may indirectly affect animal nutrient excretion. Contaminants could also affect animal nutrient excretion as these can impair animal physiology by altering animal metabolism and inducing stress. Further, the ecosystem size and structure, including community composition and biomass, can have a strong impact on the contribution of aquatic animals to the ecosystem nutrient pool. To address the complexity of these dynamics, we examined animal‐mediated elemental excretion and recycling in both stream and lake ecosystems across gradients of DOM concentration and composition, and under contaminant exposure. We sampled aquatic consumers from a range of trophic positions in Lake Erie during two seasons (Summer vs. Fall) and in naturally DOM-variable streams and lakes. We also investigated the effect of chronic exposure to silver nanoparticles (AgNPs) under environmentally relevant conditions on fish nutrient and silver (Ag) release. We found that animals can be a substantial nutrient contributor relative to other sources due to their high biomass and that their contribution changes with trophic position and season. We also detected nonlinear relationships between animal-mediated nutrient recycling and DOM concentration and composition which dampened with increasing ecological scale. Lastly, we report the first fish DOM excretion signature and Ag excretion rates under AgNPs exposure. Our results highlight the context-dependency and variability of animal-mediated elemental cycling and showcases that animals are important modifiers and conduits of elements in aquatic ecosystems.