Nitrogen (N) and phosphorus (P) budgets in a bioflocs technology (BFT) aquaculture system and a recirculation aquaculture system (RAS) during over-wintering of tilapia (GIFT Oreochromis niloticus)for 64 d were compared in the current study. Fish feed was the major input of N in both systems, specifically, 94±0 % and 82±4 % for the RAS and BFT aquaculture system, respectively. The rate of N recovery in the BFT aquaculture systems was estimated to be 48±5 % of input N, which was significantly different from that of the RAS (37±4 %). There was no significant difference between the RASs and BFT aquaculture systems in terms of P recovery rate. The regular backwashing of the drum filter and biological filter in RAS accounted for 41±2 % of input N and 39±2 % of input P. Approximately 54 % of unassimilated nitrogen N was removed by nitrification in the BFT aquaculture systems. The results from the present study suggest that nitrification may be the dominant pathway for ammonia removal in a BFT aquaculture system rather than by heterotrophic bacterial assimilation.