Spatial distribution of (238)U and (226)Ra activities in sediment columns along the Krka River and estuary, were studied using gamma spectrometry. Markedly different (238)U and (226)Ra activities between riverine, estuarine and marine sediments were observed. Distribution of these radionuclides, as well as their anthropogenic and natural origin, was evaluated by activity measurements, taking into account sedimentation rates estimated by (137)Cs distribution in sediment columns. Naturally present (238)U and (226)Ra activities were highest in riverine and lowest in marine sediments. (238)U and (226)Ra activities in historic riverine sediments revealed anthropogenic influence from town of Knin, which diminished for 15-20% in 1990s due to warfare that caused stop of industrial, agricultural and transport activities. Drainage of the flysch material naturally elevates (238)U and (226)Ra activities in the vicinity of its inflow in the upper part of estuary. (238)U and (226)Ra from the phosphate ore discharge in the port of Sibenik did not spread further in estuary, which was also confirmed by (238)U and (226)Ra activities detected in Mytilus sp. mussels' tissue.