Microbial community and composition in stormwater runoff from mixed land use land cover (LULC) catchment with ongoing land development was diverse across the hydrological stage due different environmental parameters (hydrometeorological and physicochemical) and source of runoff. However, limited studies have been made for bacterial composition in this catchment. Therefore, this study aims to: (1) quantify the concentration of fecal indicator bacteria (FIB), stormwater quality and bacterial composition and structure according to hydrological stage; and (2) determine their correlation to environmental parameters. The 454 pyrosequencing was used to determine the bacterial community and composition; while Pearson's correlation was used to determine the correlation among parameters-FIB, stormwater quality, bacterial composition and structure-to environmental parameters. Results demonstrated that the initial and peak runoff has the highest concentration of FIB, stormwater quality and bacterial composition and structure. Proteobacteria, Bacteroidetes, Actinobacteria and Firmicutes were dominant bacteria identified in this catchment. Furthermore, the 20 most abundant genera were correlated with runoff duration, average rainfall intensity, runoff volume, runoff flow, temperature, pH, organic matter, nutrients, TSS and turbidity. An increase of FIB and stormwater quality concentration, diversity and richness of bacterial composition and structure in this study was possibly due to leakage from septic tanks, cesspools and latrines; feces of domestic and wild animals; and runoff from forest, destroyed septic system in land development site and urban LULC. Overall, this study will provide an evidence of hydrological stage impacts on the runoff microbiome environment and public health perspective.