Paper covers the research of biological kinetics processes based on a multi-species model of plankton and fish interaction of the Azov Sea at low and high size considering the V erhulst and Allee effects, competition for resources, taxis, catching, spatial distribution of biogenic matter and detritus. Discrete analogue of developed model problem of water ecology, included in a software complex, were calculated using schemes of increased order of accuracy considering the partial filling of computational cells. The system of grid equations of large dimension, arising at discretization, has been solved on the basis of a two-layer variational type method – the minimum corrections method having the maximum convergence rate. Effective parallel algorithms were developed for numerical implementation of biological kinetics problem and oriented on multiprocessor computer system and NVIDIA Tesla K80 graphics accelerator with the data storage format modification of. Due to it, the reproduction processes of biogeocenose populations have been analysed in real and accelerated time.