The Curonian Lagoon is the largest coastal lagoon of the Baltic Sea. The Curonian Lagoon is a hypereutrophic water body beset with two major problems: eutrophication and algal blooms. Biological and chemical data for the study of water eutrophication and algal blooms were collected from 4 sampling points in the coastal and off-shore areas at distances of 1 km and 4–5 km from the Curonian Spit during the period from April 2007 to November 2016. The ratio of mineral nitrogen/phosphorus forms created conditions for regular Cyanobacteria hyperblooms during the summer and early autumn. Such blooms are followed by an increase in the concentration of ammonia nitrogen, pH and BOD5, their values exceeding the threshold limits for fishery water reservoirs. A distinct peak of chlorophyll a concentration was observed in the period of freshwater Cyanobacteria hyperbloom from July to September or October. During the “hyperbloom” of Cyanobacteria, their accumulation and decomposition, which was caused by a constant wind direction, also led to the local oxygen deficit and fish mortality in the coastal zone. Chlorophyll a concentration was always at the level of intensive bloom (10–100 μg/l) and over the period of 6 years (2008, 2010, 2011, 2012, 2014, 2016) it reached the hyperbloom state (above 100 μg/l). Water temperature appeared to be one of the key factors determining seasonal and long–term variability in phytoplankton abundance and, therefore, the level of eutrophication in the Curonian Lagoon.