The filtering function of soil is an important ecosystem service for groundwater and surface water protection. The efficiency of soils as a filter depends on the behaviour of pollutants in the soil and the hydrological transport processes. This paper aims to identify knowledge gaps in processes influencing pollutant behaviour in soils and their potential transport to groundwater. Currently most soil-filter function research is approached from two disciplines, one originating from agronomical/environmental sciences; one from more fundamental hydrological process research. Combining insights and approaches from both disciplines through collaboration could lead to better understanding of this complex system and enhance assessments of management strategy changes, both over the long term as well as in different climatic settings.