In November 2001, October and November 2002, the concentrations of Hg, Cd, Pb, Cr, Cu, Zn and Ni were determined in four localities of the lower course of the Jihlava River (Czech Republic). The river water, sediments of the riverbed, zoobenthos and tissues of the fish (gill, gonad, skin, dorsal muscle) were analysed. The chub (Leuciscus cephalus) was used as the ichthyo-indicator. At the same time, the stability of the fish community was evaluated using electrofishing and applying basic ichthyological methods. The work links up with previous investigation of the upper course of the Jihlava River (three localities) carried out by the authors in the same way in 1999. The aim of present study was the completion of previous investigation in the whole longitudinal river profile by monitoring selected heavy metals. The highest Cr (14.290 -77.070 mg/kg), Zn (13.600 -92.930 mg/kg) and Ni concentrations (12.290 -36.680 mg/kg) were found in sediments and their highest loading by all of the monitored metals (without Ni) was detected in the last downstream locality (Pohořelice). Zoobenthos was most contaminated by Zn and Cu (7.480 -62.690 and 8.050 -21.810 mg/kg). In the body tissues of the chubs, the highest concentrations of Cd, Hg, Cu, Zn and Ni were determined in the gills, while Pb was also high in gills but also in gonads, the skin and in the muscle tissue. Concentrations of the analysed metals in the chub muscle were (in mg/kg): Hg 0.040 ± 0.014 -0.133 ± 0.063, Cd 0.003 ± 0.002 -0.010 ± 0.004, Pb 0.045 ± 0.038 -0.768 ± 0.038, Cr 0.046 ± 0.023 -0.106 ± 0.092, Cu 0.203 ± 0.123 -0.634 ± 0.194, Zn 4.25 ± 0.84 -6.69 ± 2.95 and Ni 0.062 ± 0.018 -0.103 ± 0.030. Significant differences in the chub muscle were found concerning Hg, Pb, Cu (P < 0.01) and Cd (P < 0.05). Taking into consideration the actually valid FAO/WHO limits for human consumption of chub muscle from the investigated river section, only Hg (PTWI 2.3 kg in locality 7) and Pb (PTWI 2.0 kg in locality 4) could constitute some risk for human health. The index of diversity of the fish community was 0.825 -2.110, equitability index 0.380 -0.793, abundance 312.6 -2,106.5 fish/ha and biomass 46.7 -451.5 kg/ha. The water quality was characterized as betamesosaprobic (saprobity index 1.77 -2.18). The results of the study reveal detailed ecological data concerning heavy metals contamination of the whole Jihlava River ecosystem (water, sediment, zoobenthos, fish). The outcome of this study extends our knowledge about metals accumulation in different fish tissues (gill, gonad, skin and muscle).