Contamination of freshwater bodies by heavy metal (HM) salts is an important environmental problem. Depending on the parameters of pollution sources and the features of a water body, the fate of pollutants and their action on hydrobionts can vary within a wide range. Estimation of many factors determining the environmental consequences of pollution of a water body is necessary due to the transformation of pollutants discharged into a water body into various forms with different migration capacity, bioaccumulation properties, and toxicity. Special methods have been worked out to study the behavior of pollutants in the natural hydroecosystems. Due to the application of these methods, natural abiotic and biotic parameters of water environment can be retained. The relationship between these parameters is impossible to simulate in the laboratory. A methodology of field modeling in the mesocosms installed directly in the investigated water body was applied for the assessment of the effects of HM (Cu, Pb, Cd, and Zn) chemical form transformation in water bodies. The distribution of the HM chemical forms was changed by changing water pH. In some experiments we used also HM complexes with dissolved organic matters (DOM) such as derived malonic acids, phtalocyanines, humic substances, modeling the natural DOM with different functional groups and structures. The conditions of natural experiments was chosen previously on the basis the chemico-thermodynamical modelling of the HM state (in terms of the main inorganic and organic forms) in the water of the concrete chemical composition. The goal of this study was to estimate the influence of transformation of the HM chemical forms in the water body on the dynamics of their precipitation into bottom sediments (BS), bioaccumulation by the floating plants, and on the condition of biota (phytoplankton and zooplankton). A serious of chemical–biological experiments were carried out at the testing area in the middle part of the Novosibirsk Reservoir using four mesocosms with a water capacity (from the bottom to the surface) of 2 m3 in each at a depth of 3.5 m. One of them was the background mini-ecosystem for assessment the consequences of HM contaminations in others mesocosms at different scenario. Summarizing, the efficiency of sorption on suspension and removal of metals from the water mass into BS decreases in the series Pb > Cu > Zn > Cd. This efficiency also decreases at increasing proportion of aquaions in acidified water. HM binding with low molecular DOM, having large hydrophobic (but not polar) fragments, results in increasing of HM removal in BS, whereas its binding with humic substances plays ambiguous role for sedimentation of different HM. Plankton community plays an important role in the process of HM removal into BS. In some experiments the effect of plankton community became stronger after 8 or 9 days after HM discharge into the mesocosms. This effect was caused by a substantial increase in the population of phytoplankton organisms, which were more tolerant to the HM action, but a stable suppression of other organisms was observed. Injection of Cu complex with phtalocyanine also causes a substantial increase of phytoplankton productivity. The increase in the proportion of most toxic HM forms (aquaions) in the mesocosm with acidified water did not prevent the above-described changes in the phytoplankton community, but even accelerated this process. The zooplankton community was much more depressed under the influence of HM than phytoplankton throughout the experiment, and the change in the proportion of HM aquaions had only a weak effect on zooplankton composition. The response of the higher plants floating on the water surface was different: the increase in the proportion of metal aquaions in the solution reduced their capacity to HM accumulation (with the exception of Zn). Thus, the methodology of studying contamination of a real water body by HM is useful for understanding the regularities in their distribution and the response of different components in the solution–suspension–biota–BS system. An important result of this study is the relationship between these characteristics and the transformation of chemical forms of metals in the water body. The negative environmental consequences of metal contamination of water bodies can be stronger in the case when the proportion of HM aquaions in the solution becomes larger. Such situation is usual in acidic waters with a low salinity and low DOM content. The negative consequences manifest themselves in a decreased efficiency of HM removal from the water mass into BS, a stronger zooplankton depression, the disturbance of the structure of phytoplankton community, and decreased bioaccumulation of pollutants by macrophytes.