The estuarine movement patterns of Mugil cephalus (Mugilidae) in response to Harmful algal blooms (HABs) was investigated in the eutrophied Sundays Estuary on the warm temperate coast of South Africa. The movements of six tagged M. cephalus (31–35 cm FL) were manually tracked using a Vemco VR100 acoustic receiver over 27 days during the typical summer bloom period. Fish were released above, within and below the mesohaline zone where Heterosigma akashiwo bloom maxima are known to occur. Physico-chemical variables and chlorophyll-a biomass were collected at each fish location and at four bloom monitoring sites, which locations were based on surface water salinity of 18, 10, 8 and 5. Mugil cephalus mostly occupied the upper mesohaline to lower oligohaline zones moving with the tidal ebb and flow. Phytoplankton biomass peaked at sites with a salinity of 10 and 8, with tagged fish only briefly (<0.63% of total time free roaming) venturing into bloom maxima areas. This is the first account of small scale intra-estuary movements of a mugilid worldwide and also the first to suggest avoidance behaviour of estuarine fishes in response to HABs. More work is needed to further understand how anthropogenic threats may impact the movements of important estuarine-dependent fish species in order to prevent the possible loss of ecosystem services induced by eutrophication.