Rice is an essential diet component for a significant portion of the population worldwide. Due to the high water demand associated with rice production, improving water use efficiency and grain quality is critical to increasing the sustainability of the crop. This species includes rice varieties with diverse pigmentation patterns. Grain quality, including industrial, nutritional, and functional quality traits, of two black rice genotypes and a commercial white rice cultivar were evaluated in different locations and under different water regimes. Flooding produced higher grain weight compared to alternate wetting and drying irrigation. A high correlation was found between grain color, total phenolic content (TPC), and antioxidant activity. The black rice genotypes showed higher TPC levels and antioxidant capacity, mainly due to higher levels of cyanidin 3-O-glucoside. The phenolic profile varied between whole and polished grains, while mineral composition was influenced by location and irrigation regime. In turn, the environment influenced grain quality in terms of industrial and nutritional characteristics, with significant differences in quality between whole and polished grains. This study provides valuable information on the genotype–environment relationship in rice and its effect on grain quality, which could contribute to selecting genotypes for an appropriate environment.

Rice is a staple food grown worldwide. While white rice varieties have been extensively studied, there is limited information on the performance of pigmented rice genotypes and their tolerance to water deficit. This study evaluated nineteen black rice genotypes and one white cultivar over three years under contrasting water regimes: traditional flooding and non-flood irrigation (NFI). Genotype–environment interactions and their impact on agronomic, yield, and grain quality traits were assessed. Black genotypes under NFI showed reduced flowering and grain quality. The average yield was 31% lower than the white cultivar. Significant genetic correlations were found between grain yield and days to anthesis (DSA), grain weight (TGW), chalkiness (CHA), and translucency (TRAN), with high broad-sense heritability (H² > 0.9). Most traits exhibited high heritability (H² > 0.7), indicating strong genetic stability. Grain yield (GR) was highly and negatively correlated with percent sterility (PS) (r = −0.84) and had a heritability of 0.76. Environmental conditions significantly influenced yield, confirming the potential for selecting water stress–tolerant genotypes. These findings provide valuable insights into black rice breeding and optimizing water management practices to support sustainable production. To our knowledge, this study is the first to evaluate the performance of a diverse set of black rice genotypes across multiple seasons under contrasting water regimes in a Mediterranean environment.