The study of benthic metabolism is an interesting tool to understand the process that occurs in bottom water at wastewater stabilization ponds. Here, rates of benthic oxygen consumption and nutrient exchange across the water–sludge interface were measured in situ using a benthic chamber. The research was carried out during autumn, winter, and summer at a municipal facultative stabilization pond working in a temperate region (Puerto Madryn city, Argentina). Both a site near the raw wastewater inlet (Inlet station) and a site near the outlet (Outlet station) were sampled. Important seasonal and spatial patterns were identified as being related to benthic fluxes. Ammonium release ranged from undetectable (autumn/summer – Inlet station) to +30.7 kg-NH4+ ha−1 d−1 (autumn – Outlet station), denitrification ranged from undetectable (winter – in both sites) to −4.0 kg-NO3− ha−1 d−1 (autumn – Outlet station), and oxygen consumption ranged from 0.07 kg-O2ha−1 d−1 (autumn/summer – Outlet station) to 0.84 kg-O2ha−1 d−1 (autumn – Inlet station). During the warmer months, the mineralization of organic matter from the bottom pond acts as a source of nutrients, which seem to support the important development of phytoplankton and nitrification activity recorded in the surface water. Bottom processes could be related to the advanced degree and efficiency of the treatment, the temperature, and probably the strong and frequent wind present in the region.