Coral reef ecosystems maintain high biodiversity and have great economic value. Nonetheless, inshore coral reefs of the Great Barrier Reef (GBR) are facing threats from poor water quality due to extensive modification of coastal catchments following European settlement. Ba/Ca ratios in coral skeletons have been used to infer past water quality, but in order to use a proxy to infer past environments, it is critical to develop a firm understanding of the parameters that control the proxy. This study investigated various environmental, climatic and oceanographic factors to understand a long-term (1976 to 2016) record of biogeochemical cycling of Ba/Ca preserved in a Cyphastrea sp. coral colony recovered from near-shore Rat Island (near Port Curtis), southern GBR. Our Cyphastrea was found to have simple skeletal microstructure, similar to that of Porites, with unaltered skeletal preservation, clear annual density banding, and an extended growth history with seasonally resolved Sr/Ca signals. This combined with a wide geographic distribution make Cyphastrea coral a potential new palaeoenvironmental archive. Although Rat Island is located near the mainland and is influenced directly by discharge from the Calliope and Boyne rivers, temporal oscillations of Ba/Ca did not show peaks associated with high runoff during summers. Rather, Cyphastrea's high-resolution Ba/Ca data shows, for the first time, consistent seasonal cycles with a gradual decrease from spring through summer and gradual rise from autumn through winter. Biogeochemical cycling of Ba in the semi-confined turbid water of Port Curtis may be controlled by active or passive planktic uptake during the spring bloom stage and removal of barite minerals formed in decaying phytoplankton during post-bloom stage. The subsequent increase of Ba/Ca from autumn through winter may be attributed to reduction of phytoplankton abundance. The semi-enclosed embayment of Port Curtis has restricted water turnover with a large terrigenous runoff load that may have significant influence on phytoplankton dynamics. Our work suggests that Ba cycling, and hence, the Ba/Ca coral