The aim of this investigation is to study the algae community formed in shallow coastal waters of “The Southern Coast of the Neva Bay” reserve in the first half of summer. The paper presents the first data about the diversity of cryptogamic organisms, algae and fungi, of this state nature reserve. Algal flora contains 47 species and varieties of cyanoprokaryotes and eukaryotic algae, belonging to Cyanoprokaryota, Chlorophyta, Streptophyta, Euglenophyta, and Ochrophyta divisions. The dominating forms are сoccoid green algae, among which Pseudopediastrum boryanum var. longicorne stands out.Most algal species are freshwater planktonic forms widespread in the Baltic Sea. More than 30 species of plant pathogenic fungi from trees and grasses were found. Powdery mildew (the exciters are sac fungi from Erysiphales) and rust (the exciters are basidial fungi from Pucciniales order) are the most common plant diseases. All the plant pathogenic fungi and plant diseases identified are typical for the plant communities surveyed.