Lowland rivers and shallow aquifers are closely coupled, and their interactions are crucial for maintaining healthy stream ecological functions. To explore river–aquifer interactions and the lowland hydrological system in three Belgian catchments, we apply a combined approach of baseflow separation, impulse response modeling, and time series analysis over a 30-year study period at the catchment scale. Baseflow from hydrograph separation shows that the three catchments are groundwater-dominated systems. The recursive digital filter methods generate a smoother baseflow time series than the graphical methods. Impulse response modeling is applied using a two-step procedure. The first step of groundwater level response modeling shows that groundwater level in shallow aquifers reacts fast to the system input, with most of the wells reaching their peak response during the first day. There is an overall trend of faster response time and higher response magnitude in the wet (October–March) than the dry (April–September) periods. The second step of groundwater inflow response modeling shows that the system response is also fast and that simulated groundwater inflow can capture some variations but not the peaks of the separated baseflow time series. The time series analysis indicates that groundwater discharge to rivers is likely following groundwater level time series characteristics, with a strong trend and seasonal strengths, in contrast to the streamflow, which exhibits a weak trend and seasonality. The impulse response modeling approach from the groundwater flow perspective can be an alternative method to estimate the groundwater inflow to rivers, as it considers the physical connection between river and aquifer to a certain extent. Further research is recommended to improve the simulation, such as giving more weight to wells close to the river and adding more drainage dynamics to the model input.