The main objectives of this study were to analyze the spatiotemporal variations of water quality, fish ecological guilds and longitudinal connectivity in the weirs of Musim Stream. Fish were collected at 44 sites during spring and fall seasons for the analysis of trophic guilds, tolerance guilds, and the ecological stream health, based on FAI model. Total 33 species were observed in the stream and the dominant species were <i>Zacco platypus</i> and <i>Squalidus qracilis majimae</i>. Mean values of BOD and COD, as an indicator of organic matter pollution, showed high in the drought spring and low in fall (post-monsoon season). Also, TP showed same pattern with the BOD and COD pattern. The hierarchical clustering, based on the fish compositions, classified as three groups (up-stream, mid-stream and the down-stream). Based on the NMDS (Non-metric Multidimensional Scaling) analysis of fish abundance, high similarity was observed between S1-S5 sites, which were consistent with the results of hierarchical cluster analysis. Fish ecological guilds in the upper stream showed a high similarity between the insectivore and sensitive species, while in the middle and lower reaches, high similarity was found between the omnivore and intermediate species. Evaluations of longitudinal connectivity, based on the structural and hydrological characteristics of the weir, indicated all disconnections by the weirs, except for S15, in the spring. Stream ecological health, based on the FAI model, was significantly (<i>p</i> < 0.05, n=37) influenced by the height of overflow (<i>Hu1</i>). Overall, our study suggests that the longitudinal connectivity, based on the weir structures, flow regime and fish swimming capacity, were blocked off by the weirs in the stream. The results provide valuable insights for securing river management strategies and served as the fundamental data for stream restoration in the future.
