The sustainability of rice cultivation in the lower Syr Darya irrigated lowlands of Kazakhstan's Aral Sea region is increasingly threatened by freshwater scarcity and secondary salinization. Over three consecutive seasons (2023–2025), field experiments were conducted to evaluate rice plant responses in terms of agronomic performance and soil salinity under saline soil conditions using a conjunctive irrigation strategy involving river water, collector–drainage water, and their mixtures. It was carried out as a randomized complete block design with five irrigation variants and four replicates: V1, river water for the whole season; V2, collector–drainage water for all seasons; V3, mixed water throughout; V4, river water until full emergence then mixed water; and V5, irrigation with river water until full seedling emergence, after which collector–drainage water was applied. These consisted of irrigation-water quality, early establishment and stand survival, plant yield components, grain yield, indicators of irrigation efficiency, soil salinity profiles and ionic composition as well as shallow groundwater conditions. Irrigation-water quality consistently differed between sources: river water showed the lowest indicators for salinity and sodicity, collector–drainage water the highest, and mixed water intermediate values. Crop and soil responses showed pronounced differences consistent with these hydrochemical disparities. V1 and V4 produced the highest three-year mean grain yields of 6.56 and 6.45 t ha⁻¹, respectively, whereas V2 yielded only 0.59 t ha⁻¹. The V1 and the V4 showed minimum specific irrigation water use; whereas, it was maximum in the case of V2, but that trend reversed for water productivity. Repetitive application of collector–drainage water also caused less favorable soil salinity environments, higher ionic load and groundwater EC. In contrast, the stepwise regime in V4 preserved soil and groundwater conditions that were reminiscent of river-water irrigation conditions. The results show that continuous irrigating with collector–drainage water substantially limits rice productivity under saline field conditions. But it is not a requirement to use only water of the highest quality. Cultivation with good-quality river water in the crop establishment phase followed by mixed-water irrigation thereafter maintained grain yield equivalent to that of river-water irrigation only. These results suggest that stage-sensitive conjunctive use of river and drainage-discharge water provide a high leverage option for sustaining rice production along with reducing adverse load on already scarce freshwater resources in salt-affected irrigation systems.