Concentrations of trace elements such as Cr, Zn, Cd, Co, Mn, Cu, Ni, Pb, and Fe were investigated in water, bottom sediments, and macrophytes (Phragmites australis and Typha latifolia L.) collected from the Borków, Wilków, and Rejów water reservoirs in the Kielce Upland (Poland). The main objective of this study was to investigate the condition of water, bottom sediments, and macrophytes in selected three sedimentary basins of the Kielce Upland and to identify natural and anthropogenic factors influencing this condition. The secondary objectives were (i) to determine the contents of trace metals in water, bottom sediments, and macrophytes, (ii) to assess the quality of abiotic and biotic elements of the ecosystem based on selected criteria, (iii) to compare reservoirs in terms of pollution, and (iv) to determine the ability of macrophytes to be used as a bioindicator of water/sediment pollution. Field tests were conducted in 2021. The trace metals in water were determined by ETAAS (Cr, Cd, Mn, Cu, Ni, Pb) and FAAS (Zn), and spectrophotometry method (Fe). The trace metals in sediments and macrophytes, including Cr, Zn, Cd, Co, Mn, Cu, Ni, Pb, and Fe, were detected using ICP-OES method. Contamination of bottom sediments with potentially toxic metals was determined based on the geo-accumulation index (Igeo), contamination factor (CF), and pollutant load index (PLI). Statistical analyses were performed using the Statistica PL 13.1. The analyses showed that the accumulation of trace elements in the surface layer of the reservoir sediments increases as follows: in Borków, Cd < Co < Ni < Cu < Pb < Cr < Zn < Mn < Fe; in Wilków, Cd < Co < Cu < Ni < Pb < Cr < Zn < Mn < Fe; and in Rejow, Cd < Co = Cu = Ni = Pb < Zn < Cr < Mn < Fe. It was shown that the average distribution of metals in the bottom sediments of the studied reservoirs was as follows: Borków > Wilków > Rejów. Research has shown that the degree of trace metal accumulation increases as follows: water < sediments < macrophytes (except Pb from the reservoir in Borków).