A set of experiments were conducted in Brazil in a pilot-scale waste stabilization pond (WSP) system (a four-maturation-pond series) treating an upflow anaerobic sludge blanket (UASB) reactor effluent. Over a year and a half the pond series was monitored under two flow rate conditions, hence also different hydraulic retention times and surface loading rates. On-site and laboratory trials were carried out to assess: (i) ammonia losses by volatilization using acrylic capture chambers placed at the surface of the ponds; (ii) organic nitrogen sedimentation rates using metal buckets placed at the bottom of the ponds for collecting settled particulate matter; (iii) nitrogen removal by algal uptake based on the nitrogen content of the suspended particulate matter in samples from the ponds' water column. In addition, nitrification and denitrification rates were measured in laboratory-based experiments using pond water and sediment samples. The pond system achieved high nitrogen removal (69% total nitrogen and 92% ammonia removal). The average total nitrogen removal rates varied from 10,098 to 3,849 g N/ha·d in the first and the last ponds, respectively, with the following fractions associated with the various removal pathways: (i) 23.5–45.6% sedimentation of organic nitrogen; (ii) 13.1–27.8% algal uptake; (iii) 1.2–3.1% ammonia volatilization; and (iv) 0.15–0.34% nitrification-denitrification.