Context Nitrogen (N) and phosphorus (P) exports from rural landscapes can cause eutrophication of inland and coastal waters. Few studies have investigated the influence of the spatial configuration of nutrient sources—i.e. the spatial arrangement of agricultural fields in headwater catchments—on N and P exports. Objectives This study aimed to (1) assess the influence of the spatial configuration of nutrient sources on nitrate (NO 3 − ) and total phosphorus (TP) exports at the catchment scale, and (2) investigate how relationships between landscape composition (% agricultural land-use) and landscape configuration vary depending on catchment size. Methods We analysed NO 3 − and TP in 19 headwaters (1–14 km², Western France) every two weeks for 17 months. The headwater catchments had similar soil types, climate, and farming systems but differed in landscape composition and spatial configuration. We developed a landscape configuration index (LCI) describing the spatial organisation of nutrient sources as a function of their hydrological distance to streams and flow accumulation zones. We calibrated the LCI’s two parameters to maximise the rank correlation with median concentrations of TP and NO 3 − . Results We found that landscape composition controlled NO 3 − exports, whereas landscape configuration controlled TP exports. For a given landscape composition, landscape spatial configuration was highly heterogeneous at small scales (< 10 km 2 ) but became homogeneous at larger scales (> 50 km 2 ). Conclusions The spatial configuration of nutrient sources influences TP but not NO 3 − exports. An ideal placement of mitigation measures to limit diffuse TP export should consider both the hydrological distance to streams and flow accumulation zones.