The use of electrospun bipolar membranes (BPMs) with an interfacial three-dimensional (3D) junction of entangled nano-/microfibers has been recently proposed as a promising fabrication strategy to develop high-performance BPMs. In these BPMs, the morphology and physical properties of the 3D junction are of utmost importance to maximize the membrane performance. However, a full understanding of the impact of the junction thickness on the membrane performance is still lacking. In this study, we have developed bipolar membranes with the same composition, only varying the 3D junction thicknesses, by regulating the electrospinning time used to deposit the nano-/microfibers at the junction. In total, four BPMs with 3D junction thicknesses of ∼4, 8, 17, and 35 μm were produced to examine the influence of the junction thickness on the membrane performance. Current–voltage curves for water dissociation of BPMs exhibited lower voltages for BPMs with thicker 3D junctions, as a result of a three-dimensional increase in the interfacial contact area between cation- and anion-exchange fibers and thus a larger water dissociation reaction area. Indeed, increasing the BPM thickness from 4 to 35 μm lowered the BPM water dissociation overpotential by 32%, with a current efficiency toward HCl/NaOH generation higher than 90%. Finally, comparing BPM performance during the water association operation revealed a substantial reduction in the voltage from levels of its supplied open circuit voltage (OCV), owing to excessive hydroxide ion (OH–) and proton (H+) leakage through the relevant layers. Overall, this work provides insights into the role of the junction thickness on electrospun BPM performance as a crucial step toward the development of membranes with optimal entangled junctions.