Real wastewater was treated with a consortium of indigenous microalgae and bacteria (MaB) in sequencing batch reactors (SBR) while the hydraulic retention time (HRT) reduced from of 3 days (5 batches) to 2 days (6 batches). Biomass uptake and nitrification were the main ammonium removal pathways (about 96% for both HRTs) and phosphate levels stayed within the European limit of 1 mg P L−1. The alkalization due to lack of inorganic carbon triggered free ammonia inhibition and partial nitrification. Consequently, the total nitrogen removal could not satisfy the EU standard. Extreme pH levels (pH > 9.5) occurred more frequently in the SBR with HRT of 3 days, leading to culture collapse and biomass washout. Maintaining the pH below 8.0 seems crucial for an efficient treatment. The pH of the SBR with HRT of 2 days was more moderate, making this HRT advantageous for the single-step MaB treatment of weak wastewaters.