Suspended growth, mixed community phototrophic wastewater treatment systems (including high-rate algal ponds and photobioreactors) have the potential to achieve biological nitrogen and phosphorus recovery with effluent nutrient concentrations below the current limit-of-technology. In order to achieve reliable and predictive performance, it is necessary to establish a thorough understanding of how design and operational decisions influence the complex community structure governing nutrient recovery in these systems. Solids residence time (SRT), a critical operational parameter governing growth rate, was leveraged as a selective pressure to shape microbial community structure in laboratory-scale photobioreactors fed secondary effluent from a local wastewater treatment plant. In order to decouple the effects of SRT and hydraulic retention time (HRT), nutrient loading was fixed across all experimental conditions and the effect of changing SRT on microbial community structure, diversity, and stability, as well as its impact on nutrient recovery, was characterized. Reactors were operated at distinct SRTs (5, 10, and 15 days) with diurnal lighting over long-term operation (>6 SRTs), and in-depth examination of the eukaryotic and bacterial community structure was performed using amplicon-based sequencing of the 18S and 16S rRNA genes, respectively. In order to better represent the microalgal community structure, this study leveraged improved 18S rRNA gene primers that have been shown to provide a more accurate representation of the wastewater process-relevant algal community members. Long-term operation resulted in distinct eukaryotic communities across SRTs, independent of the relative abundance of Operational Taxonomic Units (OTUs) in the inoculum. The longest SRT (15 days, SRT 15) resulted in a more stable algal community along with stable bacterial nitrification, while the shortest SRT (5 days, SRT 5) resulted in a less stable, more dynamic community. Although SRT was not strongly associated with overall bacterial diversity, the eukaryotic community of SRT 15 was significantly less diverse and less even than SRT 5, with a few dominant OTUs making up a majority of the eukaryotic community structure in the former. Overall, although longer SRTs promote stable bacterial nitrification, short SRTs promote higher eukaryotic diversity, increased functional stability, and better total N removal via biomass assimilation. These results indicate that SRT may be a key factor in not only controlling microalgal community membership, but community diversity and functional stability as well. Ultimately, the efficacy and reliability of NH4⁺ removal may be in tension with TN removal in mixed phototrophic systems given that lower SRTs may achieve better total N removal (via biomass assimilation) through increased eukaryotic diversity, biomass productivity, and functional stability.