Tolerance limit, kinetics of nitrogen uptake and activity of nitrate reductase (NR), nitrite reductase (NiR) and glutamine synthetase (GS) enzymes of cyanobacterium Desmonostoc muscorum PUPCCC 405.10 were studied under the regime of chloroacetanilide herbicide pretilachlor. The organism was isolated from the paddy field under application of the herbicide and tolerated pretilachlor up to 10 ppm under laboratory conditions. The incubation of the cyanobacterium in 2.5 ppm pretilachlor did not cause significant effect on N uptake while supplementation of 5-10 ppm pretilachlor in medium reduced the rate of nitrate and nitrite uptake by 35-73 % with 50 % decrease in V max and no change in K m . These results indicated that herbicide did not affect the affinity of uptake system to nitrate and nitrite. In presence of herbicide, the activity of nitrogen assimilation enzymes was inhibited by 16 % for NR and 18 % for NiR. Unchanged K m and decreased V max (50-60 %) in presence of herbicide indicated non-competitive-type inhibition of the enzymes. A 50 % decrease in V max and K m of ammonium uptake indicated un-competitive type inhibition of the ammonium transport system by the herbicide. GS activity also exhibited non-competitive inhibition in presence of pretilachlor with 21 % decrease in activity with unchanged K m and 40 % decrease in V max . Likewise, decreases in nitrogenase activity by 43 % and heterocyst formation by 40 % were recorded in presence of herbicide. Results indicated that pretilachlor affected nitrogen assimilation at uptake level and interacted with nitrogen-assimilating enzymes in a non-competitive manner.