Temperature influences the physiology and general ecology of marine invertebrates, including estuarine crabs. Anthropogenic influences on the thermal regimen in estuaries and nearby environments can impact aspects of the invertebrate lifecycle, such as reproduction, recruitment and migration. Here, we use a fisheries independent survey of Blue Swimmer Crab (Portunus armatus) in an estuary heavily influenced by thermal effluent (Lake Macquarie) and a nearby reference estuary (Wallis Lake), to investigate differences in population dynamics arising from altered thermal regimes. Many reproductive traits appeared to benefit from the warmer temperatures in Lake Macquarie, including high proportions of ovigerous females, larger ovigerous females, higher egg mass index, evidence for multiple spawning, and near year-round presence of ovigerous crabs. Despite these positive impacts on reproduction, Lake Macquarie displayed a considerably lower catch rate than Wallis Lake, suggesting a much smaller population size. Critical temperature thresholds for larval survival and development, thermally-altered migration behaviour, larval advection, and density dependence, are likely contributing to high larval and juvenile mortality, and constraining population productivity in spite of warmer temperatures. While these results show the potential impacts of thermal effluent on estuarine invertebrates, they also highlight the role of other moderating factors that may perturb the influence of climate change in warming estuaries. Ongoing monitoring that spans the planned decommissioning of power stations in Lake Macquarie is essential for managing the recreational fishery, but will also provide remarkable insight into the adaptation of an estuarine invertebrate to a substantial change in thermal regime.