Groundwater is a vital resource supplying potable water, but its quality is deteriorating alarmingly worldwide. In this study, a total of 355 GW samples of 16 GW vulnerability controlling parameters were used. GW vulnerability of As and NO3− has been assessed using Logistic regression (LR), self-organizing map (SOM), and wavelet analysis in the Ganges Delta (GD) Region. The study revealed that As vulnerability was found mostly in the middle and southern parts of the GD region, whereas NO3− vulnerability was generally observed in the middle, southern, and southeastern parts. The acceptable concentrations of As and NO3− in the GW aquifers of India and Bangladesh are almost 1321 and 4321 times greater than the WHO recommendation guidelines, respectively. High to very high As vulnerability is noticed in 37% areas of the GD region, whereas 29% area comes under the high to very high NO3− vulnerability. The excessive concentration of As and NO3− in the alluvial sediments increases the GW vulnerability in the GD region. The present study suggests regular monitoring of GW aquifers using advanced instruments (fiber-optic chemical sensors, groundwater passive samplers, etc.) and spreading awareness among the people about the adverse effects of polluted water on human health.