Lack of safe water availability and access to clean water cause a higher risk of infectious diseases and other diseases as well. Heavy metals (HMs) are inorganic pollutants that cause severe threats to humans, animals, and the environment. Therefore, an effective HM removal technology is urgently needed. In the present study, a customized bipolar membrane electrodialysis process was used to remove HMs from aqueous solutions. The impacts of the feed ionic strength, applied electrical potential, and the type and concentration of HMs (Cd²⁺, Co²⁺, Cr³⁺, Cu²⁺, and Ni²⁺) on the process performance were investigated. The results showed that feed solution pH changes occurred in four stages: it first decreased linearly before stabilizing in the acidic pH range, followed by an increase and stabilization in the basic range of the pH scale. HM speciation in the basic pH range revealed the presence of anionic HM species. The presence of HMs on anion exchange membranes confirmed the contribution of these membranes for HM removal in the base channels of the process. While no clear trend was seen in the ionic strength solution, the maximum HM removal was observed when 1.5 g/L NaCl was used. The initial HM concentration showed a linear increase in HMs removal of up to 30 mg/L. A similar trend was seen with an increase in the applied electrical potential of up to 15 V. In general, the amount of HMs removed increased in the following order: Cd²⁺ ˃ Ni²⁺ ˃ Co²⁺ ˃ Cu²⁺ ˃ Cr³⁺. Under some operational conditions, however, the removed amount of Cu²⁺, Co²⁺, and Ni²⁺ was similar. The mass balance and SEM-EDX results revealed that the removed HMs were sorbed onto the membranes. In conclusion, this process efficiently separates HMs from aqueous solutions. It showed the features of diluate pH adjustment, reduction in the overall stack electrical resistance, and contribution of anion exchange membranes in multivalent cation removal. The mechanisms involved in HMs removal were diffusion and migration from the bulk solution, followed by their sorption on both cation and anion exchange membranes.