The City of Logan, Utah uses a multi-faceted, biologically based approach to wastewater treatment. The facultative lagoon system is unique because of its large size and long retention times. Over the last five years an engineered wetland has been added to provide final polishing before release. Treated effluent water is often used for irrigation of agricultural lands. We have been investigating the nitrogen dynamics in these linked systems focusing on nitrification. We found that lagoon water samples generally had potential nitrification rates near or below detection limits, too low for effective treatment of ammonia levels in the lagoons even considering the long retention times available. Several water samples revealed nitrate accumulation and these were associated with transient nitrification. Several factors contribute to the weak nitrifying activity in the lagoons. These include 1) low oxygen availability 2) low surface area available for attached growth of nitrifying bacteria 3) fluctuating and transiently low ammonium availability causing competition for ammonium and 4) high and fluctuating pH. We observed that low ammonium levels in lagoon cells are not due primarily from N loss but rather N is being transferred from inorganic to organic forms. We believe that available ammonium is depleted in the primary cells by the assimilation and growth of algae and heterotrophic bacteria. This starves the nitrifiers early in the process and they do not become reestablished in the lagoon system. Soil samples from the wetland root-zones showed evidence of coupled nitrification and denitrification but these processes are spatially localized and may not be sufficient to reduce overall N contents. Denitrification enzyme assays indicated that the root-zones of hard bulrushes have higher rates of N transformations overall. Efforts to enhance nitrification earlier in the lagoon system will be crucial in promoting coupled nitrification-denitrification and minimizing nitrogen release to surface waters.