The leading role in balance of nutrients and preservation of soil fertility belongs to biological factors which includes fixation of atmospheric nitrogen by symbiotic and free-living diazotrophs. The most significant process for agricultural practice is the nitrogen fixation which is performed by nodule bacteria in symbiosis with bean plants. Specific crop rotations with participation of bean cultures due to use of bean rizobium systems make a basis of "biological agriculture". Therefore, inclusion of symbiotic nitrogen fixation algorithms in mathematical models of production process of bean cultures, and, therefore, and in complex models of calculation of agricultural crop rotations systems with participation of bean cultures, is an important practical task. In this article, we explore and compare methods of modeling and quantitative estimation of biological nitrogen fixation by grain and forage legumes in the field environment. Different schemes and functions used to simulate the response of nitrogen fixation to biotic and abiotic factors are compared and analyzed for their relative strengths and weaknesses. Besides, divergence in current models is analyzed, and an improvement of the biological nitrogen fixation model in a complex model of production process of bean cultures is proposed.