Arsenic in rice grains poses a threat to human health for people that consume large quantities of rice. Numerous ways have been proposed to mitigate the accumulation of arsenic in rice grains. In this study a large number of rice varieties from the aus subgroup were screened for arsenic accumulation under conventional flooding as well as using the water management technique Alternate Wetting and Drying (AWD). These varieties were then sequenced to identify Single Nucleotide Polymorphisms (SNPs) and a SNP database was created to conduct genome wide association mapping to identify loci that control natural variation for arsenic accumulation. The AWD technique on average significantly reduced grain arsenic by ∼15% when compared to rice plants grown under flooded conditions. The genetic mapping study identified a number of loci involved in the accumulation of arsenic. These results indicate that AWD and breeding are potential ways to decrease rice grain arsenic.