The purposes of the study were to analyze the seasonal effects on the fish fauna and compositions including trophic guilds and tolerance guilds. For the study, we collected fish samples twice in June as premonsoon period and early September 2007 as monsoon periods in five sampling sites of the Gap Stream, and then biological oxygen demand (BOD), nutrients (TN, TP) and suspended solids (SS) were compared with the guild data along the gradient of upstream-to-downstream. Chemical water quality, based on BOD, TP, and TN degraded gradually from the upstream to downstream reach and there were about 3 fold difference between S1 and S5. Water quality was worse in the premonsoon than the monsoon, and the heavy monsoon resulted in a dilution of the polluted river by rain water, especially, in the downstream reach. Total number of fish species, based on the catch per unit effort (CPUE), showed a distinct difference between the two seasons; 30 species were sampled in premonsoon, but 23 species were sampled in the monsoon, indicating a seasonal difference in the fish fauna. Tolerant species dominated the fish community (48.3%) in the stream, and the proportions prior to physical disturbance by the monsoon rain were evidently greater in the downstream reach than the upstream. This reflected the characteristics of urban stream polluted by nutrient enrichment as shown in the BOD and TP values. Sensitive species in the premonsoon decreased from the gradient of upstream-to-downstream reach. Such seasonal modifications in the trophic and tolerance guilds were evident. In the analysis of trophic guild and habitat guild, during the premonsoon the proportion of insectivore and riffle-benthic species were largely greater in the upstream reach than the downstream, whereas the proportions were opposite along the gradient of the stream in monsoon. Thus, the patterns of chemical water quality along the longitudinal gradients reflected the premonsoon conditions of insectivores and tolerant species, indicating that summer monsoon data of fish may not match with water quality due to large physical disturbance by flow regime. Seasonal monsoon in this region as well as the chemical pollution may act as a key role influencing the fish compositions of trophic and tolerance guilds and fauna. The data collected during the premonsoon rather than the monsoon, thus, may be better predictor for a diagnosis of stream health conditions.