We examine the ecological aspects concerning the status of the surface waters in the delta of the Selenga river for the low-water conditions which have been observed since 1996. The ongoing changes in the most important indicators of the status of the waters in the river delta are assessed on the basis of results of hydrological, hydrochemical and hydrobiological investigations made by these authors in 2013–2015 and with consideration for earlier research efforts. It is established that the low-water conditions resulted in a decrease of the role of the main delta branches, Kharauz and Levoberezhnaya, in streamflow. An increase in the contribution of groundwater in the alimentation of the river led to an increase in concentrations of main ions: for the current low-water period their total content has varied from 119 to 780 mg/L, with a maximum in small delta branches in the wintertime. Changes in concentrations of biogenic elements were recorded: total phosphorus from 10 to 190 μg P/L, mineral phosphorus from 0 to 35 μg P/L, and nitrate nitrogen from 0.01 to 0.81 μg N/L. A minimum of mineral phosphorus compounds and nitrogen was observed at the time of mass development of algae. It is established that the dynamics of organic matter content is determined by changes in hydraulicity, and by the intensity of phytoplankton development. Within the long-term context, a deterioration of water regime and vegetation infill and swamping of shallow delta branches were recorded. The development level of the phytoplankton and changes in its structure point to a progressive eutrophication of the Selenga waters. According to the value of the saprobiciness index, the quality of the Selenga waters corresponds largely to the category of “moderately polluted” waters (class II and III), and it decreases at low-water periods, especially in shallow delta branches with a high population of cryptophytic algae, to the category of “polluted” waters.Keywords: delta branches, streamflow, main ions, biogenic elements, phytoplankton, water quality.