Nitrogen mass balance in waste stabilization pond system at the University of Dar es Salaam was determined using a dynamic mathematical model in order to elucidate the biological nitrogen transformation mechanisms that are effective for removal of nitrogen in this pond system. Results show that the pond system removed 4741 g/day of nitrogen from an influent load of 8036 kg/day, which is equivalent to 59% removal efficiency. The overall dominant nitrogen removal mechanism was denitrification, which was responsible for 77.5% of the removed nitrogen. Other permanent nitrogen removal mechanisms were net loss of nitrogen to sediments and volatilization, which contributed 18.2 and 4.3% of the removed nitrogen, respectively. However, sedimentation was the major nitrogen removal mechanism in primary facultative pond, which was responsible for 73.7% of the total nitrogen removed in that pond. On the other hand, denitrification was the major nitrogen removal mechanism in secondary facultative ponds (F2 and F3) and maturation pond, M, which contributed about 95.0, 89.4 and 89.1% of the total nitrogen removed from these ponds, respectively. The major nitrogen transformation routes were mineralization and ammonia uptake in the primary facultative pond F1. In secondary facultative pond F2, nitrification and denitrification were the dominant nitrogen transformation mechanisms, while in secondary facultative pond F3 and maturation pond M, ammonia uptake was the dominant transformation route. The results obtained in this work may be used as a management tool in assessing the levels of nitrogen compounds in waste stabilization ponds and thus protect the water bodies downstream.