In this study, the influence of riverbed silting on the groundwater regime in a lowland area was investigated. The study area is situated at the Rye Island (Žitný Ostrov) in Slovakia, along the Gabčíkovo – Topoľníky canal, which is part of the drainage-irrigation canal system constructed in this locality. The Rye Island is an area with very low slope (0.25 10–4) and good climatic conditions for aquatic vegetation, therefore the canals are influenced by intensive silting processes. The spatial and temporal patterns of surface water – groundwater exchange are significantly influenced by the thickness of riverbed sediments and their permeability. The aim of this study was to evaluate the thickness and hydraulic conductivity of bed sediments in the Gabčíkovo – Topoľníky canal and to examine their influence on the groundwater – surface water interaction in the area. The hydraulic conductivity of the sediments was assessed from undisturbed samples by the falling head method. The obtained data were used for numerical simulations of groundwater heads by the TRIWACO model for different drainage and infiltration resistance conditions in the area of interest. The results of this study can support the planning of canal maintenance.