Abstract The spatial and temporal patterns of surface water (SW) - groundwater (GW) exchange are significantly affected by riverbed silting, clogging or erosion processes, by altering the thickness and hydraulic conductivity of riverbed sediments. The duration of SW-GW exchange is controlled by the drainage and infiltration resistance of river bottom sediments (e.g. Andrássy et al., 2012). Generally, these two parameters primarily depend on the hydraulic conductivity and on the thickness of clogged layer. In this study the flow processes between GW and SW were modeled by model TRIWACO for different infiltration resistance and drainage resistance of riverbed sediments. The model area is situated on the Rye Island, which is a lowland area with very low slope. In this area a channel network was built up, where the flow conditions are controlled by water-gates. Because of the low slope and the system of water gates built on the channels, the riverbeds are influenced by intensive clogging processes. First, the applicability of model TRIWACO in the study area was tested by modelling the response of GW on SW level fluctuation. It was simulated, how the regulation of water level and flow direction in the channels influence the GW level, especially in extreme hydrological conditions (drought/flood), and if the GW flow direction and GW level change as it was expected. Next, the influence of channel network silting up on GW-SW interaction was modeled. The thickness of riverbed sediments was measured and their hydraulic conductivity from disturbed sediment samples was evaluated. The assessed hydraulic conductivity was used to calculate the infiltration resistance and the drainage resistance of riverbed sediments in the study area. Then, the GW level and flow direction was simulated for different infiltration resistance and drainage resistance of sediments.