Portunid crabs are an iconic, high value species in NSW, but catches are highly variable in space and time. Substantial variation in biomass is observed in both exploited and unfished populations, and environmental effects on distribution and abundance are an important factor contributing to this variability. Predicting and responding to this variability is a challenge for management and sustainability of exploited populations. We examine spatial and temporal variation in Blue Swimmer Crab (Portunus armatus) populations, over a 2.5 year trapping survey in two temperate estuaries that differ in tidal flow and riverine input. Specifically, monthly catch rates and distribution throughout the estuary are examined alongside variation in temperature and conductivity. In Wallis Lake, the shallower estuary with a restricted entrance, both water temperature and conductivity impacted abundance and distribution of crabs but there was no evidence that pulses of freshwater flow had a major impact. For a 10 °C increase in temperature the population on average shifted ~ 700 m closer to the ocean. Males were consistently located slightly further into the estuary compared to females, but there was no convincing evidence of estuarine egression in response to lower salinity. In Port Stephens, the deeper, tidal estuary, water temperature and conductivity also impacted abundance, but while males were more dispersed than females, the distribution of crabs within the estuary did not appear to be influenced by temperature, conductivity or flow. These results highlight the links between nuanced environmental relationships and estuarine geomorphology for Blue Swimmer Crab.