The surface of the Kulunda Plain is dissected by a system of ancient wide valleys, former runoff hollows, which have a very small slope (less than 1°). Rivers flow along these weakly expressed valleys, redistributing readily soluble salts throughout the territory. The regime of these rivers is characterized by a sharp and high flood wave and low (up to complete drying) runoff in the summer. The purpose of this work is to study the ion-salt system of soils of ancient runoff troughs of the Kulunda Plain, groundwater and river waters in order to identify modern processes of soil salinization. During floods, river water feeds close-lying groundwater, influencing its chemical composition. Studies of three key sites in the valleys of the Bagan (Novosibirsk region), Burla and Kulunda (Altai Territory) rivers took place in 2021–2022. Ground waters of varying degrees of mineralization (from 3.4 to 63.0 g/l) and lie close to the surface (2–5 m), which causes a wide distribution of saline hydromorphic soils in the study area. Differences in the salt state of soils in different valleys, groundwater and river waters are discussed. The degree of salinization of soils depended on their granulometric composition. The high content of physical clay contributed to the rise of salts with groundwater and their accumulation in the soil profile. A large amount of exchangeable sodium in the soil absorbing complex of the studied soils (more than 3–5 cm (eq)/kg), the predominance of easily soluble sodium salts in the soil solution with its low mineralization, as well as the alkaline reaction of the soil medium indicates the manifestation of the process of soil salinization.