ABSTRACT: The potentially lethal Chironex fleckeri (Class Cubozoa) inhabits estuarine and nearshore coastal waters in the western Pacific. The spatial scales of connectivity between C. fleckeri populations are poorly understood. Biophysical modelling of Port Musgrave, a 17 × 21 km shallow bay in tropical Australia, was used to investigate the potential for connections between populations separated by medium (10s of km) to small (100s of m) spatial scales. We measured the swimming speeds and orientations of medusae ranging in size from 4 to 12 cm interpedalial distance (the distance between two adjacent corners on the bell of the medusae). Medusae swam longshore at average speeds (5.3 ± 3.5 cm s^-1 SD) that exceeded the local average current speeds (2.7 ± 2.4 cm s^-1). These and other ecological data were used to parameterise the biophysical model. No medusae modelled as passive were advected from the bay in 14 d; <2.5% of swimming medusae were lost. When medusae swam directionally, a high percentage aggregated in shallow waters within 10s to 100s of m of the seeding locations. Newly metamorphosed medusae are likely to be retained in the bay through a combination of ‘sticky water’ (i.e. water with reduced current speeds, reduced through diversion around obstacles) in shallow complex habitats and favourable currents. C. fleckeri are vulnerable to low salinities; however, modelling a strong flood revealed higher salinity refugia in shallow water. As there was high retention within the system, we conclude that populations of C. fleckeri inhabiting shallow, semi-enclosed estuarine bays probably represent stocks. Within these stocks, swimming and favourable currents may minimise connectivity and maintain populations at multiple spatial scales.