Application of a periodical intermittent water cycle during rice cultivation proved its potential for minimizing considerable bioavailability of arsenic (As) in soil. We also propose two parametric equations, determining arsenic release from seasonal field conditions. Soil samples were determined through Raman spectroscopy and ICP-MS. The practice also alleviate stress from ultra-physiological xylem-phloem integrity of plant parts compared to conventional flooded cultivation, as observed under FE-SEM. Rice grains were analyzed for As concentrations using Synchrotron-XRF for two rice cultivar with subsequent internal and external surface topography determination under AFM showing greater amplitude of roughness in As stressed grains from conventional cultivation. Fresh plants were analyzed for biomass with pigmentation and stress regulator enzymes viz. malondialdehyde (MDA), catalase (CAT), superoxide dismutase (SOD), guaiacol peroxidase (GPX) and total protein from both conditions and found to be better in proposed cultivation method with better sustainable productivity. Isolated rhizospheric bacteria also plays crucially in arsenic uptake and metabolism.