Inhaca Island, southern Mozambique, is located towards the southerly latitudinal limits of coral reef growth. Reef development is restricted to the margins of channels which dissect intertidal flats on the Maputo Bay side of the island, and to depths of around 6 m. In contrast to lower latitude reefs, reef development is therefore both spatially and bathymetrically restricted (largely due to high turbidity levels). These natural stress levels were exacerbated, via increased freshwater and sediment discharge, during the severe floods of late 1999/early 2000. Flood impacts varied but were most significant on reefs on the inner (western) side of the island where live coral cover (LCC) decreased from 60.5% (1999) to 24.0% (2001). This is attributed to freshwater-induced bleaching. Dead in situ coral cover increased from 18.6% (1999) to 51.3% (2001). Reefs on the southern tip of the island, by contrast, were relatively unaffected. It is suggested that this largely reflects a closer proximity to the open Indian Ocean which mitigated the effects of freshwater dilution.