The sedimentation of drainage canals is a common process and its intensity depends onseveral geographical and hydrological factors. Drainage canal sediments are frequently polluted byheavy metals or other pollutants ; they need to be periodically dredged and ultimately, have to besafely disposed of. Furthermore, pollution in smaller drainages may go undetected because underthe Water Framework Directive (Directive 2000/60/EC), catchment areas < 10 km2do not requiremonitoring. We investigated the hypothesis that water resources of small sub-catchments exposed toagricultural pollutants accumulate sediment for a longer period (several years) and severely enhanceenvironmental risks. We analyzed the data on sediment mobility in drainage canals for a smalllowland catchment in Croatia during 2013–2017. We conducted sediment transport modelling foractual precipitation episodes of a 10- year return period and design precipitation of a 50-year returnperiod. The results indicated that sediments and associated copper pollution persist at the canalbottom for several years, which increases the risk of polluting groundwater and the environment ingeneral. Only copper present at the maximum downstream section of the canal has the possibility ofmoving to the recipient stream and would only be detected in catchment areas bigger than 10 km2.We proved that smaller water bodies evaluated according to monitoring standards prescribed for theclosest larger water can enhance environmental risks.