Carbamazepine (CAB) is a commonly detected pharmaceutical in the surface waters. In the present study, we evaluated the effect of humic acid (HA) and nitrogen species on the toxicity of CAB in a typical diatom Navicula sp., and its metabolic fate. The Navicula sp. showed a high sensitivity to CAB (72 h EC50 = 0.179 mg L-1). The addition of HA (< 30 mg L-1) and ammonium could promote the growth of Navicula sp. during 6 d of exposure to CAB. CAB underwent rapid dissipation in the algal culture. The degradation of CAB in Navicula sp. cultures was significantly increased by the addition of HA and higher HA contents caused more degradation of CAB. Degradation and accumulation of CAB in Navicula sp. were significantly inhibited by ammonium. Five metabolites were found and possible degradation pathways of CAB in the algal cell were proposed. Methoxylation, demethylation, glucuronidation and hydroxylation contributed to CAB transformation in the algal cell.