Groundwater and riverbank filtrate are valuable resources for drinking water production. The presence of pathogens in the environment poses a threat to drinking water quality and human health. This chapter summarizes the current approaches for evaluating pathogen fate and transport in the environment, their removal during subsurface transport in porous aquifers and the needed infection protection to achieve safe drinking water. The focus is on whole-system concepts as proposed by the (WHO, 2017) considering potential fecal sources in water resource catchments towards the point of use. We explain how microbial pathogens move through groundwater and give an overview about the traditional and novel monitoring techniques to investigate fecal contamination in water. Modelling techniques are presented for estimating the required pathogen treatment reduction by riverbank filtration or subsequent disinfection steps to achieve safe drinking water or safe setback distances. The monitoring and modelling techniques include monitoring of natural and artificial fecal indicators and host-associated genetic fecal markers (microbial source tracking (MST) markers) in surface water and groundwater as surrogates for studying pathogen treatment and transport characteristics, experimental tracer tests, analytical and numerical transport models and quantitative microbial risk assessment (QMRA). We discuss the strengths and limitations of the presented approaches.