Wastewater stabilization ponds (WSPs) are commonly used to treat municipal wastewater in the Canadian Arctic. Bacterial community structure and functionality remain mostly uncharacterized for arctic WSPs, yet are presumed important for treatment outcomes during the 3-month summer treatment season with open water in the WSPs. The objective of this study was to investigate treatment performance and related temporal and spatial changes in the structure and putative function of bacterial communities during treatment of municipal wastewater in the WSPs of Pond Inlet and Clyde River, Nunavut over two consecutive summer treatment seasons. Influent raw wastewater contained a high organic load and large bacterial communities (~9 log 16S rRNA copies/mL) belonging mainly to Proteobacteria. Although designed to be facultative ponds, both WSPs remained anaerobic with neutral pH values (7.5–7.8) throughout the summer treatment season. Water quality data showed that nutrients [measured as carbonaceous biological oxygen demand (CBOD5)], total suspended solids, and total ammonia nitrogen were progressively reduced during treatment in the ponds as the summer progressed. The pond bacterial population size and species richness depended on the pond temperature (2–18°C), with 8.5 log 16S rRNA copies/mL and the largest alpha diversities (Shannon-Wiener index of 4-4.5) observed mid-season (late July). While the phylogenetic beta diversity in raw wastewater from the two locations remained similar, pond bacterial communities underwent significant (p < 0.05) changes to dominance of Comamonadaceae, Geobacteracea, and Porphyromonadaceae. Multivariate distance based redundancy analysis and predicted gene functionalities in the microbiota agreed with water quality results that microbial removal of nutrients (e.g., CBOD5) peaked in the middle of the summer coinciding with the treatment period with the highest pond temperatures. Information from this study will be useful for further development of models to predict biological treatment outcomes, which could be used to size and assess the feasibility of WSPs in extreme climates. Higher pond temperatures resulted in optimal biological processes and nutrient removal in the middle of the summer. While it is challenging to control environmental factors in a passive wastewater treatment system there are some design considerations that could be used to optimize temperature regimes, such as the depth of the pond.