Purpose <p>Soil fertility has often been overlooked compared to salinity for rice (<i>Oryza sativa</i> L.) cultivation in coastal saline paddies. This study investigated the changes in soil fertility of coastal paddies under desalinization and quantified the joint effects of salinity and fertility on rice growth and yield under natural field conditions.</p> Methods <p>Soil and rice samples were collected from 186 coastal paddies in southwestern Korea. Soils were analyzed for salinity indices, including electrical conductivity of saturated soil paste (EC_e) and sodium adsorption ratio (SAR), and for fertility parameters, such as soil organic matter (SOM), mineral nitrogen (N), and available phosphorus (P). Correlation analysis and random forest (RF) modeling were employed to quantify the relative contributions of salinity and fertility to rice biomass and yield variability.</p> Results <p>Decreased EC_e (0.9–25.7 dS m⁻¹) was accompanied by increased SOM, mineral N, and available P. Rice biomass (0.1–3.1&#xa0;kg m⁻²) and grain yield (&lt; 0.1–1.8&#xa0;kg m⁻²) were negatively correlated with salinity and positively with fertility. RF modeling revealed that NH₄⁺ (45.4%) and available P (12.4%) predominantly influenced vegetative biomass growth, whereas SAR (13.5%) and EC_e (8.5%) were more influential for grain yield at reproductive stage.</p> Conclusion <p>These findings highlight that rice biomass and yield are co-regulated by both soil fertility and salinity under desalinization, with distinct controlling factors for each growth stage in nutrient-limited coastal soils. Managing fertility during vegetative growth and salinity during reproductive stages are crucial for sustainable rice production in nutrient-limited coastal soils under desalinization.</p>