Knowledge of trace elements content and their behavior in aquatic ecosystems is important for their sustainable use. There is a lack of such data for saline and, especially, hypersaline lakes and lagoons. Concentrations of more than 20 elements were evaluated in bottom sediments of 15 saline/hypersaline lakes and Lagoon Sivash in Crimea. An average salinity varied from 4 to 335 g/L in studied water bodies. The concentration of the trace elements varied from lake to lake. The highest variability was recorded for Cd, from 4.13 mg/kg to below the detectable level (CV = 1.463), and for Se, from 5.52 to 0.05 mg/kg (CV = 1.053). The lowest variability demonstrated by Cr, from 368 to 17 mg/kg (CV = 0.463), and by V, from 67.8 to 1.7 mg/kg (CV = 0.481). According to the found content of studied elements, all lakes were separated into three groups, and Lagoon Sivash was not included in these clusters. Salinity affected the concentration of some elements in bottom sediments, and this effect was not linear or unidirectional. In some cases, the action of other factors, often unknown, masked the effect of salinity. The geochemical background affects the structure and functioning of aquatic ecosystems, but the state of these ecosystems can significantly modify this background. An understanding of the differences in the elemental composition of bottom sediments in different lakes is possible only based on an integrated consideration of the interaction of all landscape, intra-ecosystem, and anthropogenic processes and factors that can influence this.