Heavy metals content were examined in waters, sediments and water plants of South Bohemian ponds and in waters of the rivers Luznice and Blanice. Their content in pond and river waters were affected by the geochemical character of the catchment area. It was found that agriculture production results in increasing heavy metal content in waters. The highest content in water plants was found in emergent and submerged plants, Phragmites australis showed the lowest values. Heavy metal content in pond sediments are dependent on organic matter contents. A correlation between the metal content of sediments and the pH-values of the sediment water extract was detected.