Nitrogen (N) and phosphorous (P) from human sources has impaired streams and rivers worldwide resulting in major infrastructure projects to manage agricultural and urban wastewater. Recently, diverting urban N from wastewater using biological nutrient removal (BNR) technologies has been proposed as an effective strategy to reduce harmful algal and cyanobacterial blooms. However, mechanisms regulating lotic phototrophs can be complex due to interactions between natural controls (temperature, hydrology, transparency) and anthropogenic activities. Additionally, little is known about the effects of selective N removal, particularly on phytoplankton in small streams. This thesis investigates the impact of a wastewater upgrade from tertiary (high ammonium [10-30 mg N L-1], P removal) to BNR treatment (nitrate [4-7 mg N L-1], low ammonium and P) on streams of the northern Great Plains. Applying generalized additive models in this thesis, I analyzed the spatio-temporal (50-90% deviance explained) and physico-chemical (40-80% deviance explained) responses of phototroph abundance (trichromatic chlorophyll a) and community composition (high-pressure liquid chromatography biomarker pigments) throughout the growing season (May to September). In Chapter 2, I contrasted the importance of BNR-treated discharge with natural controls in regulating suspended and benthic phototroph abundance and community composition. In Chapter 3, I quantified changes in phytoplankton abundance and community composition over six years before and after BNR. Dilution by BNR-treated wastewater caused a shift from phytoplankton to periphyton and supported only spring taxa (diatoms and some chlorophytes) in both habitats principally due to the optical properties of effluent and nitrate (Ch. 2), whereas ammonium stimulated phytoplankton, chlorophytes in particular, across the growing season before BNR (Ch. 3). However, in both studies, wastewater effects were obscured downstream by regional hydroclimate, natural phytoplankton, and land use. Together, these studies demonstrate the success of BNR in remediating eutrophic freshwaters and inform recommendations for future management, provided in Chapter 4.