<p>Exposure to naturally occurring arsenic (As) in groundwater poses serious health risks to billions of people worldwide. In this regard, our goal was to investigate the physicochemical factors influencing arsenic availability within the water-soil-crop system. To comprehend arsenic dynamics in the water-soil-crop system as well as bioaccumulation and potential health risks, groundwater, soil, and food samples were collected and analyzed by atomic absorption spectroscopy (AAS). High geogenic arsenic in water-soil-crop system of Bengal basin ranges from 68.8 to 936.8&#xa0;µg L^− 1, 4.95 to 17.1 mg.kg^− 1, and 0.38 to 2.38 mg.kg^− 1, respectively. In groundwater, arsenic is positively moderated correlated with Fe (<i>r</i> = 0.610), Mn (<i>r</i> = 0.750), and NO₃⁻ (<i>r</i> = 0.766), suggesting that the reductive dissolution of Fe/Mn (oxy-)hydroxides significantly contributes to As release. However, its negative correlation with SO₄²⁻ (<i>r</i> = -0.207) indicates that oxidation of pyrite is not responsible for release of As. The relationship of high pH, the decoupling of As and HCO₃⁻, ion exchange, and over-extraction of groundwater contribute to the dynamics of As in aquifers. The high enrichment of arsenic in the soil indicates moderate geo-accumulation in the study area. The bioaccumulation factor and daily ingestion of arsenic through food consumption were 0.172 and 0.0046, respectively. The non-carcinogenic health risk (NcHR) from groundwater and food ingestion was 81.5 and 15 times higher, respectively, based on the target hazard quotient values and carcinogenic risk from groundwater and food are 25 and 18 times higher than the recommended value (&gt; 10⁻⁴) for metal-induced cancer risk in the human body which indicates strong As contamination in groundwater and its bioaccumulation in food.</p> Graphical Abstract <p></p>