The purpose of our research is to evaluate the agroecological condition of soils under long-term irrigation (over 50 years) and to improve existing measures to slow down degradation processes by introducing phosphogypsum. The possibility of simultaneously addressing the ecological issue of using large amounts of phosphogypsum waste and the agronomic characteristics of slowing or eliminating salinisation processes in irrigated soils has been studied and justified. The research methodology was based on the comparison of different meliorative doses of phosphogypsum under the following conditions: by the amount of exchangeable sodium that should displace calcium in the calculated soil layer; by the coagulation limit; and by the absorption norm and the corresponding amount of sodium coming with irrigation water. To determine water-soluble salts (anions, cations) and pH level, a water extract was utilized. Multi-year studies to determine the impact of phosphogypsum on irrigation-salinised soils with and without irrigation showed positive changes in the anion–cation composition of water extraction, resulting in a reduction in the degree of the salinity of these soils. It was established that in chernozem soils under irrigation, the sodium adsorption ratio decreases by 74.5% compared to the control indicators, and without irrigation, by 23%. The best results in the displacement of exchangeable sodium were observed when phosphogypsum was applied at a dose calculated by the coagulation limit without irrigation and with irrigation—by the absorption norm.