Some agricultural non-point source (NPS) pollutants accumulate in sediments in the outlet sections of watersheds. It is crucial to evaluate the historical interactions between sediment properties and watershed NPS loading. Therefore, a sediment core from the outlet of an agricultural watershed was collected. The core age was dated using the 210Pb method, and sedimentation rates were determined using the constant rate of supply (CRS) model. The total nitrogen (TN), total phosphorus (TP), Cd, Pb, Cu, Ni and Cr accumulations in the sediment generally showed fluctuating increases, with the highest sedimentation fluxes all occurring in approximately 1998. The measurement of specific mass sedimentation rates reflected a record of watershed soil erosion dynamics. Using SWAT (Soil and Water Assessment Tool) to simulate long-term watershed agricultural NPS pollution loadings, the historical interactions between sediment properties and NPS loadings were further evaluated. The N leaching process weakened these interactions, but the historical accumulations of TP and heavy metals in sediments generally correlated well with watershed NPS TP loading. The regression analysis suggested that Pb and Cr were the most suitable indexes for assessing long-term NPS TN and TP pollution, respectively. Assessing the NPS loading dynamics using the vertical characteristics of sediment geochemistry is a new method.