Abstract <p>The size diversity of algal communities in the plankton of saline tributaries of the hyperhaline Elton Lake was studied based on the volume and linear parameters of alga cells. The size structure of these communities includes nanoplankton (51–68%), microplankton (16–41%), and picoplankton (7–16%). The ratio of size groups in the phytoplankton was characterized by temporal and spatial heterogeneity. Long-term observations revealed an increase in the picoplankton fraction in polyhaline rivers compared to mesohaline ones, as well as the same increase along the longitudinal river profile: from the upstream water to the mouth reach (“river–lake” contact). In spite of differences in the species composition of algal communities in different rivers, the average coenotic cell volume represents a stable and sensitive morphological parameter of these communities. A significant reduction in the coenotic volume was observed in the lower reaches and mouths of the studied rivers during periods of extreme salinity caused by the inflow of saline water from the lake. An association between the size characteristics and the content of biogenic nutrients was observed for certain species. Correlation coefficients between the size diversity indices and mineralization were higher for polyhaline rivers (0.59–0.78, <i>p</i> ≤ 0.05) compared to mesohaline ones (0.50–0.58, <i>p</i> ≤ 0.05). Thus, in the saline rivers of the basin of Elton Lake, the average coenotic volume and the ratio of size fractions can serve as informative morphological indicators of how phytoplankton communities respond to changes in mineralization.</p>