Excessive inputs of sediment and acceleration of primary production have been observed worldwide in a large number of water bodies. Human-environment interactions were recognized as one of the main drivers of this evolution during the 20th century with the occurrence of major landscape changes and a greater use of agricultural inputs. In this study, we used paleo-production proxies such as chlorophyll-a, organic matter properties (TOC and TN concentrations, δ13C and δ15N) measured in sediment cores dated with fallout 210Pbex and 137Cs activities for reconstructing changes in accumulation rates and sources of organic matter during the recent period of agricultural intensification (1920–2020). In order to record these changes at the regional scale, sediment cores were collected at the outlet of several headwater catchments (n = 9), covering a wide range of land covers / land uses across the Loire River basin (117,000 km²), France. The rates of sedimentary organic matter deposition in the studied water bodies accelerated from 1950 onwards (+48 %). Between 1950 and 1970, the signature of sedimentary organic matter indicates a dominant contribution of soil-derived inputs. This period corresponds to major landscape modifications across the basin (land consolidation, stream re-design, implementation of tile drains) driving a general acceleration of erosion rates. Then, from 1960 onwards, chlorophyll-a and C/N proxies indicate an increase in primary production coupled with a decrease of terrigenous supply in agricultural catchments. These proxies were strongly correlated to the agricultural inputs during the 1955–1990 period (e.g., r = 0.9 between chlorophyll-a content and N inputs), suggesting a progressive eutrophication of these reservoirs driven by increasing fertilizer use. During these 35 years, sedimentary organic matter deposition rates increased on average by 30 %. During the 1990s, despite a slight reduction in fertilizer use (−13 %), the paleo-production proxies (e.g. chlorophyll-a) still indicate a positive trend suggesting the contribution of another driving factor such as climate warming or again nutrient release from soils and sediments. In the absence of long term geochemical and sediment input monitoring, paleolimnological reconstructions provide a powerful tool to reconstruct past agricultural pressures in rural environments. This study illustrates the impact of intensive farming on water body siltation driven by varying sources of organic material during the 20th century. In addition, these results suggest that eutrophication processes of these reservoirs with contrasting land uses started during the 1960–1970 period and are still ongoing nowadays.