There is a growing volume of research on stormwater control measures and rehabilitation of stream habitats, but the knowledge generated was mainly from the global North. Their development and application in tropical Asia, which is ecologically less studied than and climatically differs from the more temperate regions, require more data to evaluate their effectiveness. The lower catchment of Tung Chung River (TCR), referred to as “the last remaining large-scale natural river” in Hong Kong, South China, is undergoing extensive urbanization under Tung Chung New Town Extension (TCNTE). Before the new town extension began, villages, brownfields and other built-up areas covered around one-fifth of the lower catchment. The TCNTE involves the provision of more than 12000 housing units in the remaining catchment floor of less than 0.7 km2, along with the establishment of a Sustainable Urban Drainage System (SUDS) and dechannelisation of a 600m section along one of its lower tributaries to mitigate urbanisation impacts on TCR. We collected aquatic biota and water quality data between 2018 and 2022, thus representing the period before and at the beginning of the TCNTE construction phase to establish baseline references and targets for the effectiveness evaluation of the above conservation measures. Water quality deterioration, indicated by high specific conductance and abnormal levels in pH and dissolved oxygen, was found to increase with decreasing distance from current human settlements along the lower courses. Low diversity of adult aquatic insects, extremely low density and richness of freshwater fishes, as well as the absence of certain native fish guilds were observed along the channelised section. Effective SUDS and rehabilitation should check water quality deterioration and allow recovery of aquatic taxa abundance, community structure and function amid intensifying urban growth, which are all challenging in tropical Asia due to ample knowledge gaps and rapid urbanization.