Accumulated sludge in polishing (maturation) ponds reduces the hydraulic retention time (smaller useful volume), and this could potentially lead to a decrease in performance. However, settled biomass, present in the sediments, can contribute to nitrogen removal by different mechanisms such as nitrification and denitrification. This study investigated the influence of the bottom sludge present in a shallow maturation pond treating the effluent from an anaerobic reactor on the nitrification and denitrification processes. Nitrification and denitrification rates were determined in sediment cores by applying ammonia pulses. Environmental conditions in the medium were measured and bacteria detected and quantified by real-time polymerase chain reaction (real-time PCR). The pond showed daily cycles of mixing and stratification and most of the bacteria involved in nitrogen removal decreased in concentration from the upper to the lower part of the sludge layer. The results indicate that denitrifiers, nitrifiers and anammox bacteria coexisted in the sludge, and thus different metabolic pathways were involved in ammonium removal in the system. Therefore, the sediment contributed to nitrogen removal, even with a decrease in the hydraulic retention time in the pond due to the volume occupied by the sludge.