Developing countries and the global population face a significant challenge in ensuring an adequate supply of fresh groundwater. Human activities have had a detrimental impact on groundwater, which is a crucial source of fresh water. Currently, there is growing apprehension regarding the presence of nitrates (NO3−) and trace metals (As, Cr, Ni, Pb, and Fe) in groundwater due to the extensive use of fertilizers and other human-made sources like sewage or industrial wastewater discharge. Thus, this study assesses hydrochemical characteristics that influence groundwater quality, assessing contamination levels, recharge mechanisms, and potential health risks of the Ganges Floodplain (GF) and Jamuna Floodplain (JF) in Bangladesh. A total of 105 water samples were gathered and analyzed, encompassing chemical parameters, trace metals, and isotopic composition to calculate groundwater quality. The findings indicated that the standard allowable limits WHO are exceeded by the concentrations of NO3, As, Cr, Ni, Pb, Fe, and Mn in the shallow and intermediate aquifer, while it is lower at the deep Holocene aquifer of GF and JF. Water types prevalent in the GF and JF are primarily Ca–HCO3 to Na–HCO3 types. The results of δ18O and δ2H showed how precipitation has recently recharged the Floodplain regions. The PCA was employed to discern pollution sources and controlling factors, revealing that groundwater quality is primarily influenced by geological factors and various anthropogenic activities. The IWQI indicates that groundwater from shallow aquifers is deemed unsuitable for drinking purposes in both the GF and JF. In contrast, deep Holocene aquifers are found to be suitable for drinking. Additionally, the majority of shallow groundwater samples highlight remarkable levels of pollution in JF and GF according to the HPI, HEI, and CD values. It is possible to conclude that the results of a comprehensive investigation will alert decision-makers and the local populace, empowering them to implement efficient management strategies to protect groundwater resources in Bangladesh and mitigate potential health risks for the residents.