Cell-based toxicity testing has emerged as a useful tool in (eco)toxicological research, allowing the ethical assessment of the effects of contaminants such as trace metals on marine megafauna. However, metal interactions with various dissolved ligands in the microplate environment may influence the effective exposure concentrations. Hence, the cells are not exposed to the nominal concentrations within the test system. This study aimed to establish and evaluate the effectiveness of cell-based bioassays for investigating the toxicity of selected metals in dugongs through the following objectives: (1) measure the cytotoxic potential of cadmium (Cd2+), and chromium (Cr6+) to dugong skin cell cultures, (2) investigate the interactions between media constituents and selected trace metals in cell-based bioassays, and (3) evaluate the risk to a free-ranging population of dugong based on effect values. Chromium was the most toxic of the metals tested (EC50 = 1.14 µM), followed by Cd (EC50 = 6.35 µM). Assessment of ultrafiltered (< 3 kDa) exposure media showed that 1% and 92.5% of Cr and Cd were associated with larger organic components of the media. Further, the binding of Cd to media constituents was calculated to underestimate Cd toxicity in cell-based assays by an order of magnitude. This understanding of metal partitioning in cell-based bioassays provides a more accurate method for assessing toxicity in cell-based bioassays. In addition, this study illustrated that dugong cells are more sensitive to Cr and Cd than other marine wildlife species. The chemical risk assessment found the dugong population in Moreton Bay to be at high risk from Cd exposure.