Boreholes (50 m depth) and piezometers (50 m depth) were drilled and installed for collecting As-rich sediments and groundwater in the Ganges, Brahmaputra, and Meghna flood plains for geochemical analyses. Forty-one groundwater samples were collected from the three areas for the analyses of cations (Ca 2+, Mg 2+, K +, Na +), anions (Cl −, NO 3 −, SO 4 2−), total organic carbon (TOC), and trace elements (As, Mn, Fe, Sr, Se, Ni, Co, Cu, Mo, Sb, Pb). X-ray powder diffraction (XRD) and X-ray fluorescence (XRF) were performed to characterize the major mineral and chemical contents of aquifer sediments. In all three study areas, results of XRF analysis clearly show that fine-grained sediments contain higher amounts of trace element because of their high surface area for adsorption. Relative fluorescent intensity of humic substances in groundwater samples ranges from 30 to 102 (mean 58 ± 20, n = 20), 54–195 (mean 105 ± 48, n = 10), and 27–243 (mean 79 ± 71, n = 11) in the Ganges, Brahmaputra and Meghna flood plains, respectively. Arsenic concentration in groundwater (20–50 m of depth) ranges from 3 to 315 μg/L (mean 62.4 ± 93.1 μg/L, n = 20), 16.4–73.7 μg/L (mean 28.5 ± 22.4 μg/L, n = 10) and 4.6–215.4 μg/L (mean 30.7 ± 62.1 μg/L, n = 11) in the Ganges, Brahmaputra and Meghna flood plains, respectively. Specific ultra violet adsorption (SUVA) values (less than 3 m −1 mg −1 L) indicate that the groundwater in the Ganges flood plain has relatively low percentage of aromatic organic carbon compared to those in the Brahmaputra and Meghna flood plains. Arsenic content in sediments ranges from 1 to 11 mg/kg (mean 3.5 ± 2.7 mg/kg, n = 17) in the three flood plains. Total organic carbon content is 0.5–3.7 g/kg (mean 1.9 ± 1.1 g/kg) in the Ganges flood plain, 0.5–2.1 g/kg (mean: 1.1 ± 0.7 g/kg) in the Brahmaputra flood plain and 0.3–4.4 g/kg (mean 1.9 ± 1.9 g/kg) in the Meghna flood plain. Arsenic is positively correlated with TOC ( R 2 = 0.50, 0.87, and 0.85) in sediments from the three areas. Fourier transform infrared (FT-IR) analysis of the sediments revealed that the functional groups of humic substances in three areas include amines, phenol, alkanes, and aromatic carbon. Arsenic and Fe speciation in sediments were determined using XANES and the results imply that As(V) and Fe(III) are the dominant species in most sediments. The results also imply that As (V) and Fe (III) in most of the sediment samples of the three areas are the dominant species. X-ray absorption fine structure (EXAFS) analysis shows that FeOOH is the main carrier of As in the sediments of three areas. In sediments, As is well correlated with Fe and Mn. However, there is no such correlation observed between As and Fe as well as As and Mn in groundwater, implying that mobilizations of Fe, Mn, and As are decoupled or their concentrations in groundwater have been affected by other geochemical processes following reductive dissolution of Fe or Mn-hydroxides. For example, dissolved Fe and Mn levels may be affected by precipitation of Fe- and Mn-carbonate minerals such as siderite, while liberated As remains in groundwater. The groundwaters of the Brahmaputra and Meghna flood plains contain higher humic substances in relative fluorescence intensity (or fluorescence index) and lower redox potential compared to the groundwater of Ganges flood plain. This leads to the release of arsenic and iron to groundwater of these three plains in considerable amounts, but their concentrations are distributed in spatial variations.