One of the major problems of aquatic systems in the world is their ever-growing contamination originating from different types of anthropogenic activities, such as industrial production and mining and smelting operations. Among many types of contaminants, metals/metalloids occupy an important place in the environmental studies. The obligation of European countries is to ensure the good quality of their freshwaters in accordance with European Union Water Framework Directive (EU WFD; 2000), with an aim to secure drinking water supply for the population, as well as to protect freshwater biota. To achieve this, it is common to monitor freshwater contamination with metals, i.e. to measure dissolved metal concentrations in the water as more bioavailable fraction compared to total metal concentrations, and to measure metal concentrations in the sediment, as a possible source of dietborne metals for aquatic organisms. Furthermore, it is considered as a standard research approach in the ecotoxicological assessment of metal pollution to determine the metal bioaccumulation, as well as the changes in the responses of biomarkers of metal exposure and effects (e.g. total cytosolic proteins (TP) for general stress, metallothioneins (MT) for metal exposure, total glutathione (tGSH) and catalase (CAT) for anitoxidative capacity, malondialdehyde (MDA) for oxidative damage and acetylcholinesterase (AChE) for exposure to organic contaminants and metals) in the organs of aquatic organisms, as the most effective ways to evaluate potential impacts of metals on aquatic biota. Fish and bivalves are considered as a good choice of bioindicator organisms in such studies, the first one because they are at the top of the aquatic food chain, and therefore mirror the combination of the biotic and abiotic conditions in the particular aquatic environment, and the latter one because they are sedentary organisms and known to accumulate high levels of metals and still survive. In addition, the fish liver and bivalves digestive gland are considered as recommendable target organs for the analyses, since they present the metabolic, detoxification and storage centres of their organisms. However, to obtain more complete insight in the effects of metal contamination and metal bioaccumulation in aquatic organisms, such as fish and bivalves, it is important to gather the information on metal fate in the organs and cells of bioindicators after metal uptake and distribution within their organisms. Many trace elements play important biological roles as integral parts of enzymes or protein structures. And their toxicity is also often postulated to arise from reactions in the cytosol, through nonspecific binding to physiologically important molecules and their consequent inactivation. After entering the organism, metals might be bound by a variety of biomolecules participating in the metabolic functions, storage, detoxification, toxicity mechanisms, or excretion. For many elements, biological functions and mechanisms of toxicity in aquatic organisms are still not thoroughly investigated, and the proteins to which they bind are only partially identified and characterized. A new scientific field has thus recently arisen, named metallomics, and its most important research target is elucidation of the physiological roles and functions of biomolecules binding with metallic ions in the biological systems. Metallomic analyses require sophisticated multidimensional analytical approaches, including separation techniques, such as various techniques of liquid chromatography, an elemental high sensitivity detector, such as HR ICP-MS, and a molecule-specific detector, based on mass spectrometry, for characterization of separated metal-binding biomolecules. Metallomic approaches and strategies should be more frequently used in the environmental studies to elucidate multiple new fish and bivalves metalloproteins, to discover the mechanisms that underlay the metabolic functions and toxic actions of metals, and to eventually identify new biomarkers of metal pollution. Moreover, it has been described in the literature that certain metals can cause various health problems in fish, such as immunosuppression and increased susceptibility to viral and bacterial diseases, skeletal system deformities, neoplasia, osmoregulatory dysfunctions, and pathological changes in the fish liver, which is the reason to more closely study the effects of metal pollution on fish health.