Single-walled boron nitride nanotubes (BNNTs) have been explored for various applications, ranging from water desalination to osmotic power harvesting. However, no simulation work so far has modeled the changes in the partial charge distribution when a flat sheet is rolled into a tube, hindering the ability to perform accurate molecular dynamics (MD) simulations of water flow through BNNTs. To address this knowledge gap, we employ electronic density functional theory (DFT) calculations to precisely estimate quantum-mechanically derived partial charges on boron (B) and nitrogen (N) atoms in BNNTs of varying lengths and diameters. We observe a spatially varying charge distribution inside both armchair and zigzag nanotubes of finite lengths. Performing DFT calculations for longer BNNTs is computationally intractable, even with state-of-the-art computing resources. To solve this issue, we devise a charge assignment scheme to predict partial charges for longer BNNTs using DFT data for shorter nanotubes, thus overcoming the need to perform more expensive DFT calculations. We show that these charges reproduce the electrostatic potential predicted from first-principles simulations. Subsequently, we carried out MD simulations to predict the effect of the charge distribution inside BNNTs on water flow enhancement via them. We find that using uniform charges leads to an underprediction in flow enhancement, as compared to using quantum-mechanical charges for both armchair and zigzag BNNTs. We also incorporate atomic vibrations into our simulations and show that these vibrations lead to a reduction in the water flow through aperiodic BNNTs. Our work demonstrates the requirement of a quantum-mechanical charge assignment scheme for BNNTs and evolves a framework to assign charges to nanotubes of arbitrary length, thus allowing realistic MD simulations of long BNNTs using accurate partial charges.