Freshwater ecosystems are under immense pressure from global environmental change. These stressors have led to biogeochemical alterations and rapid rates of defaunation and losses of associated animal-driven ecosystem functions. Zoogeochemistry is an ideal framework for trying to meet the dual challenges of global change and defaunation in freshwater ecosystems, but zoogeochemical frameworks that explicitly link conservation biology with biogeochemistry have not yet been fully embraced by freshwater ecologists. We conducted a systematic review and meta-analysis of the mechanistic roles that animals play in freshwater biogeochemistry, with the aim of advancing the application of zoogeochemistry in freshwaters. We reviewed 14 major mechanisms of freshwater zoogeochemistry. We grouped mechanisms into three primary categories: (1) trophic interactions that mediate the movement and transformation of elements through food webs, (2) metabolic processes, including excretion and egestion, that directly alter nutrient availability, and (3) physical ecosystem engineering, such as bioturbation and sediment resuspension, which modify redox conditions and enhance benthic–pelagic coupling. Our review shows that a diversity of taxa impact ecosystem-level elemental pools and fluxes of dozens of elements including the traditional macronutrients, C, N, and P, and a range of micronutrients, both within and across freshwater ecosystem boundaries. However, these effects are not always placed in context at the ecosystem level, which limited the scope of our meta-analysis. Zoogeochemical impacts tended to be stronger in wetlands and lakes than streams and freshwater estuaries. Consumption, excretion, and respiration had the strongest direct impacts on elemental pools and fluxes; bioturbation, consumption, and egestion had the strongest indirect impacts. These mechanisms often interacted, generating complex influences on elemental pools and fluxes. However, creative experimental designs can be used to isolate individual mechanisms, allowing complex effects with multiple mechanisms to be incorporated into ecosystem models. Anthropogenic pressures such as biodiversity loss, altered species interactions, habitat fragmentation, and climate-driven shifts in movement and phenology, are disrupting animal-mediated biogeochemical processes at local and landscape scales. Quantifying and modelling zoogeochemical effects in freshwater ecosystems will allow ecologists and managers to make informed decisions that balance biodiversity conservation with healthy ecosystem function.