A model of symbiotic nitrogen fixation by nodule tissues of roots is an essential part of a comprehensive and integrated approach to modeling the production process of legumes. Its implementation as a part of AGROTOOL crop productivity simulation model is explained by specific biological features of legume crops. Due to the symbiosis with rhizobia (legume bacteria), legumes acquire the ability to assimilate nitrogen from air. This fact plays an important role in a nitrogen nutrition of plants and maintaining of soils fertility. Specific crop rotations with legumes using legume-rhizobium systems are the basis of the “biological agriculture”. Therefore, symbiotic nitrogen fixation algorithms are required for mathematical models of legumes production and complex models of agricultural crop rotations with legumes. It is an important practical problem. Modeling of nitrogen transformation processes in soil and nitrogen absorption by plants will help to control crops development and attain highest possible yields using nitrogen fertilizers efficiently and, thereby, reducing nitrogen pollution. The research goals are development and experimental validation of the symbiotic nitrogen fixation model.