Abstract Bioactive trace elements play an important role in metabolic processes and, ultimately, marine productivity. An understanding of the complex interactions between biogeochemical processes and trace elements in reef ecosystems is important for establishing geochemical proxies for marine productivity or biological activity. In an attempt to illustrate this relationship, concentrations of dissolved trace elements (V, As, Se, W, and Y), dissolved oxygen (DO), and carbonate system parameters were measured over diurnal cycles on the Luhuitou fringing reef, located in the northern South China Sea. Prominent diurnal variations in DO and carbonate system parameters indicate that biological activities, especially photosynthesis and respiration, are the primary controls on reef water chemistry. The trace elements V, W, and Y co-varied significantly with seawater pH and DIC, implying that they participate in community photosynthesis and respiration. In contrast, As and Se demonstrated divergent diurnal to semi-diurnal behaviors, and their concentrations were not correlated with carbonate system parameters, suggesting that they were involved in other biogeochemical processes. The biologically controlled behaviors of V, W, and Y suggest that their records could potentially serve as geochemical proxies for marine productivity.