Mountain wetlands in Mediterranean regions are particularly threatened in agricultural environments due to anthropogenic activity. An integrated study of source-to-sink sediment fluxes was carried out in an agricultural catchment that holds a small permanent lake included in the European NATURA 2000 Network. More than 1000 yrs of human intervention and the variety of land uses pose a substantial challenge when attempting to estimate sediment fluxes which is the first requirement to protect fragile wetlands. To date, there have been few similar studies and those that have been carried out have not addressed such complex terrain. Geostatistical interpolation and GIS tools were used to derive the soil spatial redistribution from point (137)Cs inventories, and to establish the sediment budget in a catchment located in the Southern Pyrenees. The soil redistribution was intense and soil erosion predominated over soil deposition. On the areas that maintained natural vegetation the median soil erosion and deposition rates were moderate, ranging from 2.6 to 6 Mg ha yr(-1) and 1.5 to 2.1 Mg ha yr(-1), respectively. However, in cultivated fields both erosion and deposition were significantly higher (ca. 20 Mg ha yr(-1)), and the maximum rates were always associated with tillage practices. Farming activities in the last part of the 20th century intensified soil erosion, as evidenced by the 1963 (137)Cs peaks in the lake cores and estimates from the sediment budget indicated a net deposition of 671 Mg yr(-1). Results confirm a siltation risk for the lake and provide a foundation for designing management plans to preserve this threatened wetland. This comprehensive approach provides information useful for understanding processes that influence the patterns and rates of soil transfer and deposition within fragile Mediterranean mountain wetlands subjected to climate and anthropogenic stresses.