Pollution with nitrogen (N) and phosphorous (P) impairs streams by favoring suspended algae and cyano- bacteria over diatom-rich periphyton. Recently, wastewater treatment plants have been upgraded to biological nutrient removal to eliminate both P and N (mainly NH4+), although little is known of the effects of this effluent on flowing waters. Here, we used high performance liquid chromatography to quantify how the abundance and composition of phytoplankton and periphyton varied in response to both influx of effluent produced by biologi- cal nutrient removal and physico-chemical conditions in small, turbid, P-rich streams of the northern Great Plains. At the catchment scale, analysis with generalized additive models (GAMs) explained 40.5–62.6% of devi- ance in total phototroph abundance (as Chl a) and 72.5–82.5% of deviance in community composition (as biomarker carotenoids) in both planktonic and benthic habitats when date- and site-specific physico-chemical parameters were used as predictors. In contrast, GAMs using wastewater input (as aqueous δ15 N) as a predictor explained up to 50% of deviance in Chl a, and ~60% of deviance in community composition, in both suspended (51.6% of Chl a, 67.1% of composition) and attached communities (21.5% of Chl a, 58.8% of composition). Phy- toplankton was replaced by periphyton within a 60-km wastewater-impacted reach due to dilution of streams by transparent effluent and addition of urban NO3 , although predominance of phytoplankton was re-established after confluence with higher-order streams. Overall, influx of effluent shifted turbid, phytoplankton-rich streams to clear ecosystems with abundant epilithon by improving water transparency and providing NO3 to favor benthic diatoms and chlorophytes.