There are few territories around the world where water availability does not limit the yield of agricultural crops. As a rule, water is the main natural limiting factor, and either water deficiency or its surplus restrict the yield level. Attempts were made to establish the relations and simulation methods enabling an estimate of the influence of water deficiency stress on the yield formation. An opposite situation, when plants grow under overmoistening conditions, is not investigated. The aim of this paper is to propose a method of simulation of water stress index which unifies the influence of both water deficit and excess on plant growth and development and on the final yield. New method of the simulation of plant transpiration under submergence conditions was proposed and the dynamic simulation model of water balance under agricultural crop was developed for this purpose.