On results the long-term researches conducted in 1988-2008 the estimation of dynamics of biodiversity the nestingbirds’ community of Molochny estuary was performed. The breeding birds’ community of reeds, saline lands, sandyislands and spits, arboreal-shrub jungles were estimated. Is is proved that the gulls, terns, cormorants and passerineswere the dominant species during the period of high water. Maximum specific variety was also proved for this timeperiod. In drought seasons of 2001-2010 the water level in estuary went down sharply that had resulted in the decline ofbiodiversity and amount of breeding birds. Negative trend of biodiversity level was discussed.