The natural occurrence of arsenic (As) in groundwater & soils and its bioaccumulation in rice grains is a major health concern worldwide. To combat the problem, best combination of irrigation management and suitable rice variety altering As content in grains must be ensured. With this aim, a field trial was conducted with two rice varieties and water management including alternate wetting and drying (AWD) and continuous flooding (CF) irrigation regimes with As contaminated groundwater (AsW) and temporarily stored groundwater (TSG) and river water for only CF (as control). Results revealed that As content in different portions of paddy plant was significantly different (P < 0.001) with irrigation practices and rice varieties. AWD irrigation with TSG accumulated lower As in rice grains compared with CF-AsW for both varieties. Data showed that AWD-TSG practice led to 61.37% and 60.34% grain As reduction for BRRI dhan28 and BRRI dhan29, respectively, compared with CF-AsW. For Principle Component Analysis (PCA), first principle component (PC1) explained 91.7% of the variability and irrigation water As, soil total and available As, straw As, root As and husk As were the dominating parameters. With significant (P < 0.05) variation in yields between the genotypes, AWD increased grain yield by 29.25% in BRRI dhan29 Compared with CF. However, translocation factor (TF) and bioconcentration factor (BCF) for both varieties were less than one for all the treatments. The addition of this study to our knowledge base is that, AWD-TSG with BRRI dhan29 can be an As–safe practice without compromising yields.