A submersible in situ spectrofluorometer, which permits the differentiation of four algal groups (green algae, diatoms, cryptophytes and cyanobacteria), was used for phytoplankton monitoring in five reservoirs with varying levels of eutrophication and composition of their phytoplankton communities. Data obtained in situ were compared to standard laboratory methods for phytoplankton quantification; concentration of chlorophyll a and microscopy analysis. A high correlation (r = 0.95, n = 96) between chlorophyll a levels using different methods was found in all types of phytoplankton community. Taxonomic analyses and cell counts were closely related to the ratio of algal classes measured by the in situ spectrofluorometer. The submersible device used in the study measures in a continuous mode, which is advantageous in comparison with discrete sampling. This method appears to be a good tool for water quality management and can be used in the detection of natural horizontal and vertical variability in phytoplankton communities or for the early detection of cyanobacterial blooms. The device used in this study is recommended as a screening tool that enables more effective sampling that can be focused on the localities and depths where changes in phytoplankton composition occur.