Many ray species are threatened with extinction, and so understanding their movement and habitat use is vital for developing effective management and conservation efforts. Globally, rays are known to rely on estuarine habitats, but estuary use by rays has not yet been investigated in South Africa. Thirty-three diamond rays Gymnura natalensis and 25 bull rays Aetomylaeus bovinus , both species anecdotally recorded to occur in estuaries, were acoustically tagged. Individuals were tracked using a nation-wide network of receivers in South Africa, the Acoustic Tracking Array Platform (ATAP), that has acoustic receivers in both marine and estuarine environments. Only six rays (4 diamond and 2 bull rays) were recorded using estuaries, but they displayed seasonal philopatry, returning to specific estuaries during spring to autumn months (September to May) for up to 6 consecutive years. Due to a number of rays entering the Breede Estuary, the fine-scale habitat use in this ecosystem was investigated. Marine-estuarine connectivity was significantly influenced by marine temperatures. Additionally, presence in the upper parts of the Breede Estuary (up to 17 km from the mouth) was influenced by temperature, tides and time of day. Findings suggest estuaries are an important, and previously overlooked, habitat type for a portion of the diamond and bull ray populations on the south coast of South Africa, which has management and conservation implications.