The upstream of Lanyang River is intensively exploited for agricultural activities. This study aimed to determine temporal and spatial pattern of abundance and community of epilithic periphyton along the main stream and effects of agricultural activities to determine the main deriving factors. The results from a 2-year study show that greater abundance of epilithic periphyton was observed in the upstream with agricultural activities than a tributary without the activities. Regression analyses show that velocity was the main factor determining the abundance in the river. Faster velocity (60 cm s^-1) led to greater abundance of epilithic periphyton. Results of MDS show that the periphyton community was structured by site rather than by season. Epilithic periphyton was dominant by Cymbella sp. in an upstream tributary without agricultural activities and the mid-stream, where DIN concentrations in the water column were lower and velocity was slower. The dominance shifted to Cladophora sp. and Nitzschia palea in the upstream with higher DIN concentrations and faster velocity. Cyanobacteria, especially Lyngbya sp., were dominant in two tributaries with higher DIP concentrations. In summary, nutrients and velocity were the main factors influencing abundance and community of epilithic periphyton in Lanyang River.