Abstract: The paper analyzes the variation features of water environment of the Pearl River estuary in recent 20 years and researches with the interrelation and interaction of water environment and aquatic biology of the estuary. The results indicate that the variations of morphology,geomorphy,hydrological regime and water pollutants have changed the perching conditions of aquatic living things of the estuary,decreased self regulation and restoration capability and homeostasis of ecosystem,influenced greatly on matter cycle,energy transfer,development,evolution and equilibrium in the ecosystem of the Pearl River estuary.