The article is aimed at developing and testing a methodology for collecting information to calculate the diffuse input of nitrogen and phosphorus from agricultural land to water bodies using the IEEP model due to the lack of detailed information on individual agricultural enterprises in relation to the conditions of the Lake Onego catchment. The methodology enables obtaining comprehensive information about agricultural objects, taking into account their impact on the environment. The methodology is based on the use of spatial analysis and GIS technologies to calculate the load more accurately, considering the characteristics of agricultural activities and distance to water bodies. Thus, one can perform a comprehensive analysis in relation to the spatial parameters of the environment. The methodology provides the calculation of the volume and composition of manure, considering systems for its storage, processing and application, as well as assessment of the nutrients migration parameters depending on the location of agricultural land. Based on the results of the agricultural objects analysis in the GIS, in view of available information, the number of animals and poultry, the production of manure, as well as the number of manure storage facilities at the enterprise, the average application rates of nitrogen and phosphorus with organic fertilizers are quantified. The proposed methodology was implemented in the Lake Onego catchment to prepare data for calculating the nitrogen and phosphorus diffuse load in 2010 and 2021. The IEEP methodology helped to assess and compare nutrient input from agriculture to the Lake Onego water objects in 2010 and 2021.