The development of concepts concerning the stability of aquatic ecosystem and their variation under conditions of toxic pollution and after its reduction is considered. General trends in ecosystem transformation are explained in terms of theoretical ecology and thermodynamic mechanisms of energy ordering in living systems. Basic symptoms of disorganization in ecosystems under extreme loads and of their regenerative self-organization are discussed. It is shown that the development of a new modification of an aquatic ecosystem after a decrease in toxic pollution complies with the pattern of ecosystem succession: from a natural ecosystem, via the critical stage, to its more stable but structurally different modification.