In this study, a municipal lagoon with high wintertime effluent total ammonia nitrogen (TAN) concentrations was upgraded with a pilot-scale nitrifying-nitrifyingdenitrifying (NIT-NIT-DENIT) moving bed biofilm reactor (MBBR) treatment train to characterize its effluent over wintertime operation, investigate the feasibility of upgrading lagoons to achieve substantial biological total nitrogen removal across ultra-low temperatures (0.6 -3.0°C) and investigate nitrification inhibition pathways in facultative lagoon systems at ultra-low temperatures. Throughout the study, it was observed that the system substantially reduced total nitrogen (TN) and total phosphorus (TP) effluent concentrations by an average of 69.8 ± 24.5% and 74.7 ± 20.1%, respectively. Furthermore, it was observed that sulfide toxicity may play an important role in the inhibition of nitrifying organisms in lagoons. Finally, the MBBR treatment technology has emerged as a suitable and sustainable upgrade technology for existing lagoon and waste stabilization pond facilities operating in temperate, northern, and cold climate countries.