Estuaries are dynamic and their physical and chemical characteristics can change over a scale of hours to years. Consequently, estuarine fish assemblages often exhibit large temporal variations in abundance and composition related to changes in a range of parameters such as river flow, estuarine mouth phase, habitat availability, temperature, salinity and turbidity, all of which are likely to be highly affected by climate change. Many organisms become more stressed towards their range boundaries and the distributions of these species can be expected to shift as environmental conditions change. Preliminary studies have highlighted the increased occurrence of tropical fish species in estuaries along the southeast coast of South Africa. Climate change is also predicted to alter precipitation patterns, which will affect the quality, rate, magnitude and timing of freshwater delivery to estuaries, and will potentially exacerbate existing human modifications of these flows. This is likely to result in changes to fish communities, as river flow has been found to have a major impact on the structure and functioning of fish communities in South African estuaries. The predicted increase in the frequency of extreme weather events, together with sea level rise, may result in a loss of estuarine habitat, which will ultimately affect estuarine fish communities and have implications for fisheries targeting estuary-associated species.