The Amsterdam area, a highly manipulated delta area formed by polders and reclaimed lakes, struggles with high nutrient levels in its surface water system. The polders receive spatially and temporally variable amounts of water and nutrients via surface runoff, groundwater seepage, sewer leakage, and via water inlets from upstream polders. Diffuse anthropogenic sources, such as manure and fertiliser use and atmospheric deposition, add to the water quality problems in the polders. The major nutrient sources and pathways have not yet been clarified due to the complex hydrological system in lowland catchments with both urban and agricultural areas. In this study, the spatial variability of the groundwater seepage impact was identified by exploiting the dense groundwater and surface water monitoring networks in Amsterdam and its surrounding polders. A total of 25 variables (concentrations of total nitrogen (TN), total phosphorus (TP), NH4, NO3, HCO3, SO4, Ca, and Cl in surface water and groundwater, N and P agricultural inputs, seepage rate, elevation, land-use, and soil type) for 144 polders were analysed statistically and interpreted in relation to sources, transport mechanisms, and pathways. The results imply that groundwateris a large source of nutrients in the greater Amsterdam mixed urban–agricultural catchments. The groundwater nutrient concentrations exceeded the surface water environmental quality standards (EQSs) in 93% of the polders for TP and in 91%for TN. Groundwater outflow into the polders thus adds to nutrient levels in the surface water. High correlations (R2 up to 0.88) between solutes in groundwater and surface water, together with the close similarities in their spatial patterns, confirmed the large impact of groundwater on surface water chemistry, especially in the polders that have high seepage rates. Our analysis indicates that the elevated nutrient and bicarbonate concentrations in the groundwater seepage originate from the decomposition of organic matter in subsurface sediments coupled to sulfate reduction and possibly methanogenesis. The large loads of nutrient-rich groundwater seepage into the deepest polders indirectly affect surface water quality in the surrounding area, because excess water from the deep polders is pumped out and used to supply water to the surrounding infiltrating polders in dry periods. The study shows the importance of the connection between groundwater and surface water nutrient chemistry in the greater Amsterdam area. We expect that taking account of groundwater–surface water interaction is also important in other subsiding and urbanising deltas around the world, where water is managed intensively in order to enable agricultural productivity and achieve water-sustainable cities.