The arsenic contamination in soil-water-plant systems is a major concern of where, the groundwater is being contaminated with arsenic (above 0.01 mg/L) in the Indian subcontinent. The study was conducted with organic matter to find out the reducing effect on arsenic load to rice (cv. Khitish). It was observed that intermittent ponding reduced arsenic uptake (23.33% in root, 13.84% in shoot and 19.84% in leaf) at panicle initiation stage, instead of continuous ponding. A decreasing trend of arsenic accumulation (root > straw > husk > whole grain > milled grain) was observed in different plant parts at harvest. Combined applications of lathyrus + vermicompost + poultry manure reduced arsenic transport in plant parts (root, straw, husk, whole grains and milled grain) which was significantly at par (p > 0.05) with chopped rice straw (5 tons/ha) + lathyrus green manuring (5 tons/ha) in comparison to control and corresponding soils. A significant negative correlation of arsenic with phosphorus (grain P with arsenic in different parts R2= 0.627-0.726 at p > 0.01) was observed. Similarly, soil arsenic had a negative correlation with soil available phosphorus (R2 = 0.822 at p > 0.001) followed by soil nitrogen (R2 = 0.762 at p > 0.01) and soil potassium (R2 = 0.626 at p > 0.01). Hence, effective management of contaminated irrigation water along with organic matter could reduce the arsenic build up to plants and soil.