Few measurements of nitrogen fixation exist for streams. Desert streams are warm, well lighted, and often support abundant cyanobacterial populations; thus N-2 fixation may be significant in these N-poor ecosystems. N-2 fixation was measured in situ by acetylene reduction for two patch types (Anabaena mat and an epilithic assemblage). Patch-specific rates were high compared with published values (maximum 775 mu g N-2 [83 mu mol C2H4] mg chl a(-1) h(-1) or 51 mg N-2 [5.4 mmol C2H4] m(-2) h(-1)). Daytime fixation was higher than nighttime fixation, and temperature, light and inorganic N concentration explained 52% of variance in hourly rates over all dates. Diel input-output budgets were constructed on five dates when cyanobacteria were present in the stream. Diel N-2 fixation rates were measured for comparison with reach-scale diel nitrogen retention, to assess the importance of this vector to N economy of the stream. Fixation accounted for up to 85% of net N flux to the benthos, but its importance varied seasonally. Finally, we applied biomass-specific fixation rates to 1992 and 1993 biomass data to obtain seasonal and annual N-2 fixation estimates. Cyanobacteria were absent or rare during winter and spring, thus most of the annual N-2 fixation occurred during summer and autumn. Annual rates of nitrogen fixation for 1992 and 1993 (8.0 g/m(2) and 12.5 g/m(2)) were very high compared to other streams, and moderately high compared to other ecosystems. Like other phenomena in this disturbance-prone ecosystem, nitrogen fixation is strongly influenced by the number and temporal distribution of flood events.