The distribution of heavy metals in sediments of the Nemunas river have been investigated. The most obvious anthropogenic impact has been observed in the middle part of the river. Nevertheless, sediment metal concentrations are within the limits of global, regional and local concentration levels. Particular attention has been paid to the Kaunas Reservoir. Although it is a part of the river, sediment characteristics, including metal distribution, have been found to follow the bottom dynamic zones, as in lakes. Metal concentrations in the Kaunas Reservoir are close to the concentrations in the upstream part of the Nemunas river, without indicating increased contamination with metals due to the lower flow velocity. An unusual Fe/Mn ratio is characteristic to the Reservoir. Fe concentrations confirm the occurrence of anoxic hypolimnion, whereas Mn concentrations indicate the possibility of Mn transport from the nearshore sediments to the deepest places.