Metal contamination is an ever-increasing threat to marine organisms, yet ecotoxicological assessments still mostly rely on total metal concentration determinations, which overlook the distinction between toxic bioavailable metals and detoxified intracellular pools. In this sense, bioactive cytosolic and mitochondrial metals drive oxidative stress and metabolic disruption, whereas sequestration in lysosomes or granules reduces toxicity. This mini-review highlights the importance of subcellular metal compartmentalization and the analytical tools employed in its assessment, indicating the need for integration in improving toxicity prediction, biomonitoring accuracy, and environmental risk assessments.