This study was conducted over a five-month period at Rawan Oya, a 13.5km long left bank tributary of the River Mahaweli. Data on species composition and mircohabitat conditions were collected from 30 random sampling sites, representing 10 pools, 10 riffles and 10 runs. A single observation was made at each site, where a 10m-length of the stream was blocked with drag nets to get the values for abundance. Fishes were captured using the cast nets and scoop nets, identified and released back at the site of capture. The species richness, relative abundance and the microhabitat conditions were recorded for each habitat type. Physico-chemical parameters of water such as the stream velocity, temperature, pH, water depth, conductivity, Hardness, DO and BOD 5 were determined monthly at pre-selected sampling sites. A questionnaire survey was done among people in adjacent villagers, who are selected randomly. A total of 15 fish species belonging to 8 families were recorded of which 2 are endemic and 4 are exotic. The subsequent data analysis revealed that the Shannon Wiener diversity index and the Magalef Index are significantly high in pools. ANOVA test showed significant variation among the 3 habitat types in terms of the microhabitat features measured. Further, the Pearson Correlation test demonstrated that the different fish species have different microhabitat preferences and different habitat associations. Runs seemed to be the most suitable habitats for most of the fish species lotic habitat with the highest species richness compared with the other two habitat types (12 species). Riffles harbored the poorest in species composition (2 species). Pools had an intermediate number of species (9). Puntius bimaculatus, Hypostomus sp and Tor khudree only occurred in pools while Devario malabaricus, Glossogobius giuris, Lepidocephalichthys thermalis, Mystus vittatus, Rasbora daniconius and Xiphophorus maculatus are confined to runs of the stream with no species confined to riffles. Garra ceylonensis and Schistura notostigma occupy all three kinds of habitat types but with higher abundances in riffles. Among the fish found only in pools and runs, Puntius filamentosus were recorded in significantly higher numbers in pools than that in runs in contrast to the alien species such as Poecilia reticulata and Oreochromis mossambicus that showed a higher preference for runs.