As can be seen by the amount of actions taken by several international organizations, the need for safe drinking water is becoming more and more evident. Since the quality of drinking water sources is decreasing, old and new methodologies are being used to improve the quality of the source water. One of these old methods is riverbank filtration (RBF). RBF systems are relatively inexpensive and are able to produce water which is relatively consistent in quality and usually easier treatable. Processes like adsorption, biodegradation and physicochemical filtration are responsible for the increase in water quality during aquifer passage. Not only these processes, but also the quality of the infiltrating surface water is of importance for the eventual quality of the groundwater. Therefore, the focus of this doctoral thesis was on the influence of surface water on both the chemical and microbial quality of the aquifer. The combination of chemical and microbial parameters is crucial due to the increasing global contamination of surface waters with these contaminants. Many RBF systems are situated along rivers with a high dynamics in water levels and in chemical and microbial water quality. It is of paramount importance to get an insight in this dynamics, since processes taking place in the aquifer can be influenced by it. RBF systems along large rivers like the Danube provide drinking water for millions of people. The dynamics in RBF systems along large rivers can be much higher than in RBF systems connected to for example lakes. Together with the increasing anthropogenic activities in many of the (sub-)catchments, the stress on the groundwater is increasing. Organic micropollutants (OMPs) and microbial contaminants are introduced to the environment through for example wastewater treatment plant (WWTP) effluents and can have serious health effects. Their behaviour during aquifer passage is different, just as their analysis. The aim of this doctoral thesis is therefore to elucidate the influences of surface water infiltrating into the aquifer, on one hand on the microbial community naturally found in the groundwater and on the other hand on the behavior of OMPs during aquifer passage. The highest biological activity, and therefore the fastest removal of contaminants, can be found in the first few meters of the aquifer. It is therefore crucial to obtain samples representative for the surrounding aquifer, especially close to the river. Along a highly dynamic river like the Danube, this can be a challenge since stabilization of parameters might not be as quick as the changes in water levels. Therefore, chapter 2 discusses the effect of pumping volume on the concentration of OMPs and microbial contaminants amongst others in a highly dynamic RBF system along the river Danube. Samples were taken after different pumping volumes, both close to the river as well as further into the aquifer. It was found that both the fluctuations in groundwater table and the fluctuations in contaminant concentrations did not affect the stability of the obtained chemical samples. Microbial parameters such as leucine incorporation (which is a measure for the biological activity of the microbial community) however did show a significant relation between stabilization and pumping volume. With this information at hand, chapter 3 discusses the influence of surface water on the microbial characteristics of the aquifer. The response of the microbial community on seasonal dynamics, nutrient stimuli and hydrological fluctuations was studied during a 20 months period including 2 flood events which were sampled more extensively. The results showed that bacterial abundance, biomass and carbon production decreased significantly from the river towards the drinking water abstraction well. This was not influenced by the availability of nutrients or by seasonal dynamics, but mainly by fluctuations in groundwater flow velocity. During the flood events, this correlation was even more apparent and it could be seen that the rivers influence extended further into the aquifer, as was shown by a much higher proportion of larger cells in the groundwater during flood events than under normal conditions. In chapter 4, the behavior of OMPs during RBF was studied. The samples were drawn over a slightly longer period than described in chapter 3 and also included the 2 flood events. The OMPs showed a likewise extended influence of the river during the two flood events. Some highly degradable OMPs were not found in the groundwater, whereas concentrations of common wastewater markers benzotriazole (BTri), carbamazepine (CBZ) and sulfamethoxazole (SMZ) were higher than under normal conditions. It was shown that in this oxic aquifer, BTri was almost fully removed under normal conditions. CBZ and SMZ, which were assumed to have a rather conservative behavior during aquifer passage, were attenuated to a certain extent. Mixing with groundwater of a better quality could not solely explain this decrease in concentration. This thesis showed that obtaining samples for a combination of chemical and microbial parameters was not an easy task. Furthermore, wells especially close to the river and situated in oxic aquifers with high hydraulic conductivities can react quickly on changing hydrological conditions. One of the most important parameters for the extent of the surface water groundwater interaction was shown to be the potential difference between the river water and groundwater level. Not only the presence of OMPs can be influenced, also the microbial community can be altered by the infiltrating river. Since microbiological characteristics and the potential difference can be measured (near) real-time, this could be a very effective way for drinking water utilities to manage their abstraction strategies during periods of high discharge and rapidly changing hydrological conditions.