Sexual segregation seems to be common in bottlenose dolphins, whereby males and females live in different pods that mix mainly for mating. Male dolphins often use aggressive behaviour to mate with females, while females with calves may have different activity and dietary requirements to males and different susceptibility to predation. We investigated the degree of spatial and social sexual segregation in Indo-Pacific bottlenose dolphins (Tursiops aduncus) in a subtropical estuary in Australia. Based on surveys completed over three years, dolphin groups were mostly mixed-sex or female. Mixed-sex groups were found in larger groups in mostly deeper water, whereas, female groups were foraging across all water depths in smaller groups. Aggressive coercive behaviour by males towards females was high, occurring mainly in deeper water, at higher tides, and outside the breeding season. Habitat use by female dolphin groups suggests that shallow tributaries may provide a sanctuary from aggressive males, access to suitable prey items and density for mothers and their calves, or a combination of these factors.