Swine wastewater was treated in two continuously aerated activated sludge (AS) systems at high (AS1: 1.7–2.6 mg/L) and low (AS2: 0.04–0.08 mg/L) dissolved oxygen (DO), and at three temperatures (10, 20, and 30 °C). Biochemical oxygen demand (BOD) removal was >94.8%. Meanwhile, total nitrogen (N) removal was significantly higher in AS2, at 64, 89, and 88%, than in AS1, at 12, 24, and 46%, for 10, 20, and 30 °C, respectively. The experimental data were considered in a simulation study using an AS model for BOD and N removal, which also included nitrite, free ammonia, free nitrous acid, and temperature. Simulations at high-DO showed that ammonium was partly oxidized into nitrate but not removed, whereas at low-DO ammonium was removed mainly through the nitrite shortcut in simultaneous nitrification–denitrification. This study demonstrates that treatment at low-DO is an effective method for removing N, and modelling a helpful tool for its optimization.