Sequencing batch reactors (SBRs) with floating biofilm carriers are a promising option for small dairy plants, because nitrification and denitrification can proceed simultaneously in one reactor at a low dissolved oxygen (DO) concentration. Total nitrogen (TN) removal alone, however, does not show how much nitrogen is converted to N2 and how much leaves with the excess sludge. To assess these pathways, a dynamic model based on Activated Sludge Model No. 3 was developed, with two-step nitrification, limited substrate storage, apparent oxygen half-saturation constants for simultaneous nitrification–denitrification in flocs and a lumped biofilm limited by the carrier surface. Nitrogen and COD balances agreed to within 0.003%. The model was checked against two experimental studies published by other groups; both used synthetic wastewater, so this validation is preliminary. After two apparent constants were calibrated on a DO series in a continuous hybrid reactor, the model reproduced TN removal at C/N 8–10 without further calibration (RMSE 5.7 percentage points), but not at C/N 4 or at low DO, where nitrification in the real reactor was impaired. For an aerated moving-bed SBR it reproduced the sludge concentration (within 3–12%) and end-of-cycle nitrate at COD/N 10 but overestimated nitrification. Scenario simulations for dairy wastewater (COD 2000 mg/L, sludge age 15 d) showed that the share of nitrogen removed with the excess sludge increases from about 12% at COD/N 10 to 58% at COD/N 45, while the share converted to N2 decreases accordingly. Carriers had almost no effect on overall TN removal with the literature nitrification kinetics but at COD/N ≥ 30 reduced the share of nitrogen bound in the sludge. When nitrifier growth rates were lowered so that the simulated residual ammonium approached the measured values, the share of nitrogen in the sludge changed by at most 2.2 percentage points. Without carriers, however, nitrifiers washed out at DO ≤ 1 mg/L and most of the remaining nitrogen left as effluent ammonium instead of N2; with carriers nitrification was maintained at DO 1 mg/L. For dairy wastewater rich in organic matter, TN removal alone therefore cannot show which part of the nitrogen was actually denitrified.