Biogeochemical rates within streams vary with ecosystem properties including the distribution of fishes. While many studies investigate the singular effect of fishes on ecosystem components, there is a limited understanding of how fish presence interacts with other ecosystem properties to affect ecosystem structure and function. Here, we used path analyses to elucidate direct and indirect effects of fish presence, and other ecosystem properties on ecosystem respiration (ER), gross primary production (GPP), and ammonium uptake. Experimental responses of fish removal on patch scale (300 cm2) benthic rates of ER, GPP, and ammonium uptake were measured at two sites in a prairie stream. The effect of fish was determined by comparing substrata from field exclosures with fish absent to substrata exposed to fish. Total path model-explained variance was greatest for ER (R2 = 0.55) and least for ammonium uptake (R2 = 0.36) and GPP (R2 = 0.34). Fish decreased algal biomass and directly increased all biogeochemical rates. The relative importance of the different abiotic ecosystem properties varied by process; however, FBOM and substrata size were important for most rates. This study provides evidence for predominantly direct effects of fish on both stream structure and function in a prairie stream. Our results emphasize that interactions between biotic and abiotic factors should be considered when determining drivers of biogeochemical activity. We suggest that simple linear food webs that consist of top–down or bottom–up control are not always sufficient to describe animal effects on ecosystem rates.