As active ingredients of anti-fouling paints that are widely used on ship hulls, organotin compounds, in particular tributyltin (TBT), are well-known endocrine disruptors causing sex changes in marine organisms and widespread in coastal waters and sediments worldwide. In this study, a comprehensive ecological risk assessment (ERA) of organotins was conducted in Hong Kong waters through determining the imposex status, sex ratio and tissue burdens of these compounds in the neogastropods, Thais clavigera and Thais luteostoma collected from 29 coastal sites. We also investigated the historical trend of organotin effects on these gastropods, and performed a probabilistic ERA based on tissue burden of TBT in the animals. Our results demonstrated that imposex indices were positively correlated with the body burden of organotins in the gastropods. Across all sites, the sex ratio (female:male) decreased significantly with increasing imposex levels or tissue burden of organotins, implying that such pollutants can result in a male-biased population, potentially leading to local extinction in extreme cases. Based on the ERA, 5.4% of all populations of T. clavigera are at risk due to exposure to TBT; the risks include growth inhibition, impairment of immune functions and reduced fitness. Seriously impacted areas included Aberdeen, Repulse Bay, Butterfly Beach, Mui Wo and Ha Mei Wan. A comparison with historical data revealed that there had been some improvement in the areas with low marine traffic, and distant from the major harbour/port. This could partly be due to the restriction on the use of TBT on small vessels (<25m in length) since 1992. Nevertheless, the organotin contamination still remains severe in areas with high marine traffic or adjacent to large harbours/ports. In particular, the situation in the northeastern waters of Hong Kong has been getting worst since 1996 that is probably associated with the rapid development of the cargo container port at Yantian in China.