The Tapee River is the longest river in Southern Thailand. Data from five years (2015-2019) of fish monitoring at five sampling stations along the lower reach were used to examine variation in fish diversity and fish assemblages through diversity analyses and multivariate techniques. Sampling was conducted every three months, representing the dry and wet seasons as well as two transition periods. One hundred and eight (108) fish species were recorded, including freshwater, brackish-water and marine species. The samples were dominated, both in terms of species richness and abundance, by fishes from family Cyprinidae. No significant differences in four diversity indices (species richness, Shannon–Weaver H’, abundance, and evenness J’) were found by either spatial or temporal approaches. The W-statistic from abundance-biomass curve suggests heavy disturbance of most fish communities. During the rainy season and dry-to-rainy transition, fish assemblages in the lowermost station near the river mouth clearly differed from assemblages in the upper stations. Results can be used as a baseline for resource management to maintain the integrity of the Tapee River.