Despite estuary-to-estuary differences in assemblage composition, fish faunas of tropical Indo-Pacific estuaries show parallel patterns of temporal change, suggesting a common set of ecological drivers. One potentially important driver is the interaction of different patterns of occupancy by functional groups that display different life-history patterns. However, most studies that have considered temporal change lack the detail needed to understand life-history utilisation. Most have focussed on changes in catch per unit effort (CPUE) or probability of encounter, with only one study going further and investigating changes in size structure and then only for a single estuary. One of the reasons for this lack of detail is the large volume of work needed to collect comprehensive data on size structures of species rich assemblages across multiple estuary systems over time. To overcome the logistical limitations on data collection, we used joint patterns of change in CPUE and mean biomass per fish (BPF) as proxies for changes in size structure. We investigated how different life-history strategies contributed to overall temporal patterns of assemblage change across four tropical Indo-Pacific estuaries. The three life-history strategies displayed characteristically different patterns in CPUE and BPF and the relationships between CPUE and BPF that reflect differences in the way that the three groups use estuaries. These different patterns interacted to produce complex assemblage patterns that are likely to be sensitive to location-specific differences in the mix of species from each group, providing at least part of the explanation for the site-specific fish assemblage structures that are characteristic of tropical estuarine fish fauna.