<p>The Songnen Plain in Northeast China is a global hotspot for soda saline-alkalization. This region suffers from severe water security challenges that limit agricultural productivity. Our assessment reveals severe irrigation hazards in the local saline-alkaline water. These waters show prevalent alkaline conditions with pH values ranging from 8.04 to 9.50. The dominant water type is NaHCO₃, with extreme sodicity levels. Importantly, 63.3% of water samples were classified as C4S4 (EC &gt; 2250 µS cm⁻¹, SAR &gt; 26), indicating extreme hazard. These samples exceeded sodium hazard thresholds by 2.3–4.8 times. Hydrochemical analysis identified silicate weathering, cation exchange, and evaporative concentration as key processes driving water quality deterioration. Importantly, rice-crab co-culture systems, particularly with juvenile crabs, effectively transform these constraints into opportunities for sustainable agriculture. The juvenile crab system achieved comprehensive improvements, reducing SAR by 41.25%, alkalinity by 1.21 mmol/L, and sodicity (%Na⁺ = 58.05), while increasing rice yields by 10.61% and total economic output by 84.51% compared to rice monoculture. A key finding was the consistent association between crab activity and concurrent RSC increases with sodium leaching, providing a new perspective on interpreting water quality indices in integrated systems. Our findings establish rice-juvenile crab co-culture as an effective nature-based solution that simultaneously addresses water security and agricultural productivity in soda saline-alkaline regions.</p>