<p>Rice is an important human staple food providing calories and useful elements, even though vulnerable to heavy metal contamination. Breeding tools for improving the concentration of nutrient and reduce levels of toxic compounds can improve the nutritional value and safety of rice grains. This work presents a comprehensive analysis of the genetic bases controlling variation in the rice ionome employing genome-wide association studies (GWAS) with a diversity panel of 294 temperate and tropical <i>japonica</i> accessions, each genotyped with 36,830 SNP loci. GWAS was performed for brown rice content of 13 elements: As, Ca, Cd, Cu, Fe, K, Mg, Mn, Mo, Na, Ni, P, Zn for rice plants grown under two diverse water management regimes, permanent flooding and limited watering. GWAS identified 232 significant marker-traits associations (MTAs); 87 of which had high R² and low p-values and were selected for further analysis. Among them, 32 MTAs were consistently identified under both environments. These can represent valuable candidates for marker-assisted selection to improve the composition of essential mineral nutrients and reduce the concentration of toxic elements in the rice grain. Furthermore, co-localization regions for 60 MTAs were highlighted for two or more traits. Potential candidate genes were identified for 14 MTAs with -log₁₀(<i>p</i>) value &lt; 5 and R² &gt; 6; among them, gene functions that were related to transport/uptake, accumulation, detoxification, metal binding and root architecture, coherent with the traits of interest, were highlighted. The study provides relevant insights into the genetic basis of ionomic variations in rice and may serve as an important foundation for improvement in breeding, as well as for further studies on the genetic bases and molecular mechanisms controlling the rice grain ionome.</p>