We monitored the effects of wastewater treatment plant (WWTP) inputs on the recovery of stream biofilms after a large flood event that eroded most of the former biofilm communities. We monitored biomass recovery, chlorophyll a, nitrogen content, and stable isotope natural abundance (15N) over 8 weeks in light‐ and dark‐exposed biofilms upstream and downstream from WWTP inputs, respectively, as well as the abundance of ammonia oxidizers by quantitative polymerase chain reaction. Biomass and chlorophyll a recovered quickly (< 2 weeks), and were significantly higher for light‐ than for dark‐exposed biofilms. There was no consistent effect of WWTP inputs on these parameters, except for the biomass on dark‐exposed biofilm that was higher at the WWTP‐influenced sites. The influence of the WWTP inputs on stream‐water ammonium concentration and its isotopic 15N signature increased as the flood receded. Biofilm 15N downstream of WWTP increased over time, tracking the increase in 15N‐ammonium from the WWTP waters. Bacterial and archaeal ammonia oxidizers were present within the biofilm assemblages from early stages of postflood recovery. However, spatial distribution of these two clades was clearly segregated among sites and between light‐ and dark‐exposed biofilms, probably related to ammonium availability and the development of photoautotrophic organisms.