The study of spatiotemporal distribution of aquatic communities was conducted in the shallow part of littoral zone of Petrokrepost Bay of Lake Ladoga for three years (from 2010 to 2012). The study covered three types of habitats gradually changing as depth increased: the littoral reed beds, zone of emergent vegetation, dominated by Potamogeton perfoliatus, and unvegetated zone (sand). The morphometric description and characteristics of macrophytes in Petrokrepost Bay are presented. It is shown that different habitats which are closely located (within hundreds of meters) are more similar in terms of aquatic species composition than the same habitats separated by tens of kilometers. The following aspects have been studied: spatial heterogeneity in the distribution of aquatic organisms; active and passive circadian horizontal and vertical migrations of mesoplankton, benthos, bacterio- and phytoplankton, and protozoa. The set of abiotic and biotic factors affecting the distribution of different groups of aquatic organisms has been detected.