This study assessed the effects of tidal stages and habitat conditions on nekton assemblage and distribution in the Kakum River estuarine mangrove system in the Central Region of Ghana. Teleosts and crustaceans were sampled using pole seine and cast net from a tidal mangrove pond and a channel, and characterised using morphometry and ecological guilds concept. In total, 1 146 specimens were collected, with 35 species from 19 families represented. The most abundant species encountered were Liza spp. (Mugilidae; 36%), Sarotherodon melanotheron (Cichlidae; 16%), Elops lacerta (Elopidae; 6%) and Sardinella aurita (Clupeidae; 5%), which exhibited pronounced spatial distribution. Sarotherodon melanotheron showed preference for ponds with minimal water flow and depth, Sardinella aurita occurred only in deeper sections of the mangrove channel with significant flow velocity, and Elops lacerta in the pond and all channel stations. Mugilids were found exclusively in the channel, whereas Palaemonidae (Macrobrachium macrobrachion and M. vollenhoveni) occurred in specific locations in the channel, with species- specific preferences for tidal stages. Most species encountered were identified to be predominantly marine migrants with bentophagous feeding habit. Site selection and tidal stages were found to affect the occurrence and distribution of fishes over a tidal cycle and interactively influence species diversity.