Arsenic (As) in rice agroecosystems causes a loss of both rice yield and quality of rice grains. In this study, an integrated approach of biochar (BC) and alternative water management is proposed to reduce As content while sustaining essential elemental concentrations in rice. The rice cultivar, Jayanthi, was grown, irrigated with 1 mg L−1 of As-containing water, under rice hull BC (RBC)-flooded, RBC-intermittent, conventional flooded, and intermittent treatments. The RBC has increased rice yield by 11%−19% in RBC-intermittent and -flooded treatments compared to the flooded treatment. Inorganic As content in rice tissues and abundance of Fe(III) reducing bacteria in the rhizosphere were lowered by 10%−83% and 40–70%, respectively, in RBC-flooded, -intermittent, and intermittent treatments over flooded treatment. Essential elemental concentrations (Fe, Mn, Zn, Mg, and Ca) in unpolished rice grains increased by 45%−329% in RBC-flooded and -intermittent treatments compared to flooded treatment. Overall, the integrated approach of RBC-intermittent practices has lowered inorganic As concentration in unpolished rice grains, while sustaining the levels of essential elements in rice grains, compared to other treatments. An integrated approach of RBC-intermittent practices is suggested for rice grown with As-contaminated water to improve the quality of rice, as well as tackling food-related malnutrition in people.