Nitrogen removal in biofilm waste stabilization ponds were modeled using nitrogen mass balance equations. Four pilot-scale biofilm maturation ponds were constructed in Uganda. Pond 1 was control; the others had 15 baffles in each of them. Two loading conditions were investigated (period 1, 18.2 g and period 2, 26.8 g NH(4)-N d(-1)). Total nitrogen and TKN mass balances were made. Bulk water and biofilm nitrification rates were determined and used in the TKN mass balance. Results for total nitrogen mass balance showed that for both periods, denitrification was the major removal mechanism. Nitrogen uptake by algae was more important during period 1 than in period 2. The TKN mass balance predicted well effluent TKN for period 2 than period 1. This could be due to fluctuations in algae density and ammonia uptake during period 1, no conclusions on reliability of mass balance model in period 1 was made. (C) 2010 Elsevier Ltd. All rights reserved.