In order to find the segments of Pinios River which lack the retention capacity of the BOD and nutrient input, the difference of the estimated input and output pollution loads was compared at upstream and downstream clustered areas of a total of 73 segments. Catchment areas ranged from 1 to 11,300 km(2). Emissions were always higher than the actual transport, therefore retention was assumed to take place. Specific runoff, percentage of the surface water area and the calculated input of pollution loads (BOD, P, N) varied between the different Pinios River basin catchment areas. The transport to the emission load ratio was different between large and small catchments. The rate of retention among consecutive segments revealed that four lowland segments lacked in their relative retention capacity. (C) 2009 Published by Elsevier B.V.