Arsenic (As) assessment in agricultural soils and corresponding crops is necessary from the global health safety perspective. To the best of our knowledge, we are reporting for the first time, As flux determining parametric equations for paddy field with seasonal rice cultivation under conventional flooding and dry-wet irrigation approaches. Rigorous field experiments and measuring quantitative parameters, flushed out or percolated into the deeper soil As flux was assessed. A wintery (boro)-monsoonal (aman) study from 2016 to 2019 has been conducted showing the efficiency of dry-wet irrigation on reduction of soil As bioavailability. The reduction in boro was 52.4% in 2016 to 64.8% in 2019 while in aman, it was 61% in 2016 to 74.9% in 2019. Low bioavailability was correlated to plant’s internal vascular structure that was found more rigid and firm in dry-wet field grown plants. Observed soil physico-chemical parameters clearly influenced As bioavailability as well as soil microbial community. Assessment of microbial diversity using metagenomics under altered water regime was done by population analysis, relative abundance, species richness, Krona chart comparison. Dry-wet field was found to be more diverse and enriched in microbial community than that of the flooded soil indicating an affective reduction of As bioavailability under biotic-abiotic factors.