This study aimed to investigate the seasonal variation of microbial quality in urban waterbodies along urbanization gradients. Bimonthly samples were collected from 14 recreational lakes and flood mitigation ponds in the Klang Valley, Malaysia, between May and October 2017. Samples were analysed for the presence and abundance of Escherichia coli, Clostridium perfringens, faecal coliforms (FC), faecal streptococci (FS), enterococci and total coliforms as indicator organisms, using standard methods. All studied lakes contained indicator bacteria that exceeded the National Lake Water Quality Standards (NLWQS) to varying degrees. The mean of the FC/FS ratios in all lakes exceeded four, indicating that the faecal contamination might have originated from human sources. Escherichia coli, C. perfringens and faecal coliform concentrations were negatively correlated with temperature (P < 0.01) and positively correlated with turbidity and suspended solids (P < 0.05). Non-parametric test results revealed that only the density of C. perfringens varied significantly according to season and urbanization impacts (P < 0.05). The Secchi depth transparency and dissolved oxygen (DO) levels explain the largest variation in bacterial communities. This study showed that contamination of faecal bacteria in the waterbodies varied spatially and temporally along urbanization gradients. Water quality monitoring and improvements are needed before the waterbodies can be used for direct body-contact recreation and as alternative water sources for drinking purposes.