The reservoirs of the Ob basin change from a river bed to an additional reservoir and further to flood plain lakes of various flood stages. This process is accompanied by changes in the composition and quantitative development of plankton and benthos communities. In terms of species composition and productivity flood plain lakes at the minor flood stage are the most diverse ones. These reservoirs along with the flood plain inundated during the flood are of fundamental importance for the processes of fattening and reproduction of freshwater fish, which makes up the bulk of fishery. Long-term investigations have revealed certain peculiarities of the dynamics of the state of aquatic community caused by natural factors. Using multivariate statistical analysis methods researchers have discovered that flood plain lakes at the minor flood stage display the repeating pattern of the long-term dynamics of invertebrates’ communities. This is determined by the dynamic combination of the two main limiting factors (hydrologic and temperature behaviour). The analysis shows the influence of these factors on the population dynamics of the fry of the fish spawning in the inundated flood plain and the further formation of the resources.