Soil erosion, as a significant contributor to nonpoint-source pollution, is ranked top of sediment sources, pollutants attached to sediment, and pollutants in the solution in surface water. This paper is focused on the design of mathematical model intended to predict the total content of nitrogen (N), phosphorus (P), and potassium (K) in bottom sediments in small water reservoirs depending on water erosion processes, together with its application and validation in small agricultural watershed of the Tisovec River, Slovakia. The designed model takes into account the calculation of total N, P, and K content adsorbed on detached and transported soil particles, which consists of supplementing the soil loss calculation with a determination of the average nutrient content in topsoils. The dissolved forms of these elements are neglected in this model. Validation of the model was carried out by statistical assessment of calculated concentrations and measured concentrations in Kľušov, a small water reservoir (Slovakia), using the t-test and F-test, at a 0.05 significance level. Calculated concentrations of total N, P, and K in reservoir sediments were in the range from 0.188 to 0.236 for total N, from 0.065 to 0.078 for total P, and from 1.94 to 2.47 for total K. Measured nutrient concentrations in composite sediment samples ranged from 0.16 to 0.26% for total N, from 0.049 to 0.113% for total P, and from 1.71 to 2.42% for total K. The statistical assessment indicates the applicability of the model in predicting the reservoir’s sediment quality detached through erosion processes in the catchment.