As the human population increases, wastewater nutrient inputs to waterways will also increase. These inputs are known to lead to eutrophication and/or hypoxia. Sewage treatment plants (STP) constantly discharge nutrients, concentrations of which are reduced due to the activated sludge process. STP operators are also testing more energy-efficient processes which reduce and/or transform the characteristics of effluent nutrients. However, the role of microbial communities in receiving waters, such as rivers, in transforming STP nutrients has received little attention. This study examined microbial communities in the Bremer River in southeast Queensland, to determine the effect of STP effluent inputs on the community and compared these results with the effect of a large rainfall event contributing diffuse catchment inputs. This study found that STP discharge did not change the microbial community structure in the river, but rainfall-runoff events did. Building on these field studies, microcosm experiments were conducted to determine the effect of STP effluent addition on the microbial community response in river samples over a few days. The study found that the microbial community composition was significantly different in composition, and diversity was lower than the river water or the STP effluent alone. These findings suggest that nutrients in the STP effluent could be driving microbial species composition within the receiving waters. This is likely to affect ecosystem functioning in the river, with implications for ecosystem health.