Detailed information on the development of phytoplankton and physical-chemical composition of water from the large river of East Siberia – Aldan was first received. The knowledge on taxonomic composition of plankton algae of the northern river is significantly replenished. Basic patterns of the spatial structure in the taxonomic structure and quantitative development of phytoplankton of the Aldan are found. Integrated assessment of water quality from the river according to bioindicative properties of plankton algae and hydrochemical parameters was made. The data received about the structure of phytoplankton and physical-chemical parameters of the Aldan waters are background and would serve the basic information for biomonitoring of the river ecosystem.