The aim of this study was to assess mercury (Hg), cadmium (Cd) and lead (Pb) contamination in muscle tissue of fishes over the longitudinal profile of the River Morava (Czech Republic, Danube basin) and to detect any temporal trends over the past 18 years. Fish samples were collected in 1992, 1998, 2000, 2003 and 2009 at 6 study sites situated just downstream of important pollution sources. Chub (Leuciscus cephalus L.) were selected as indicator species at 5 sites, and brown trout (Salmo trutta m. fario L.) at the uppermost site where chub do not occur. In total, muscle tissue of 175 specimens of chub and 19 specimens of brown trout were analysed. Concentrations of heavy metals ranged as follows: mercury 0.015-0.369 mg/kg; cadmium 0.001-0.254 mg/kg and lead 0.006-1.505 mg/kg. Mercury levels did not exceed the maximum allowed concentration in the Czech Republic (0.5 mg/kg). Content of cadmium and lead in fish muscle exceeded the maximum allowed levels (0.05 and 0.3 mg/kg respectively) in 11 and 4 samples, respectively. On average, the order of metal concentration in fish muscle was: Hg>Pb>Cd. No significant differences were found between sites along the longitudinal profile of the river. Significant differences were found, however, for the interannual comparison of cadmium and lead (but not mercury) at different sites (P < 0.05). A catastrophic flood in 1997 resulted in an increase in metal concentrations, especially cadmium and lead, in the following 1998 season. Our results indicate that the Morava river basin does not represent a threatening source of mercury, cadmium or lead for the River Danube downstream.