Subcellular fractionation is an interesting technique to study metal cell compartmentalization and helps on evaluating the impact of a contaminant in an organism. It provides a better understanding about the fate and behaviour of metals within cell compartments, being then able to identify if metals experience a detoxification process or, on the contrary, they are trophically available. Having this information about metals and metalloids is crucial in the context of risk assessment, as it provides valuable information about their behaviour throughout the food chain at different trophic levels. Coastal and marine environments are often affected by dangerous spillages. Pollutants tend to accumulate in water, soils and sediments, where they can become readily available to species, such as bivalves and fish. These species are often used as bioindicators as they can provide information about the trophic transfer and/or the accumulation and of different pollutants. After a bibliographic search, the protocols used to study the subcellular fractionation on bivalves and fish exposed to metals have been highlighted. This literature mini review focuses on the different protocols used for studying this issue and the improvements that subcellular fractionation has brought to the topic. Nonetheless, future research needs and perspectives are pointed out as they can improve the robustness of using such techniques for risk assessment.