<p>Boron (B) toxicity represents a significant form of abiotic stress that negatively affects plant development, photosynthesis, and cellular metabolism. This study evaluated the protective effects of calcium–L-aspartate nanoparticles (Ca-NPs) against B toxicity in hydroponically grown rice seedlings. Seedlings were exposed to 1 mM B, with or without Ca-NPs (at a concentration of 100 mg L^− 1) supplementation. Excess B significantly inhibited seedling growth, reduced chlorophyll and carotenoid contents, and led to excessive B accumulation in shoots and roots. It also triggered oxidative stress and disrupted antioxidant balance. Ca-NPs treatment mitigated these effects by enhancing shoot and root growth, restoring pigment content, reducing B accumulation, and enhancing antioxidant defense through increased catalase (CAT), peroxidase (POD), and reduced glutathione (GSH) levels. Furthermore, Ca-NPs regulated proline metabolism by upregulating P5CS and P5CR while suppressing ProDH activity, thereby enhancing osmoprotection. In root tissues, NPs increased pectin content and pectin methylesterase (PME) activity while reducing pectin-degrading enzymes, contributing to balanced cell wall remodeling and reduced B toxicity. These results demonstrate that Ca-NPs confer multi-layered protection against B stress by modulating physiological, biochemical, and cell wall traits, providing a potential nanotechnology-based strategy for improving plant tolerance to micronutrient toxicity.</p>