The interplay between mechanical and electrochemical forces is important to the bulk flow and transport of ions through varying natural, synthetic, and biological pores. In the current article, we demonstrate that the phase offset between the sinusoidal surface charge modulations and geometric undulations in a corrugated nanochannel provides a tunable mechanism for flow gating and rectified, diode-like ion transport under pressure-driven or electric-field driven conditions. To demonstrate these physics, the fully coupled and non-linear Poisson–Nernst–Planck–Stokes equations are solved numerically and reveal an underlying two-regime structure. At low driving force (Regime I), throughput is suppressed below the Poiseuille limit by a localized streaming potential that pins counterions within the electric double layer; at high driving force (Regime II), above a threshold pressure, the mechanical force overcomes electrostatic resistance, producing an abrupt, orders-of-magnitude rise in mean velocity. Electroosmotically driven flow undergoes a qualitatively similar but smoother transition. For mechanically driven flow, reversing the applied pressure gradient activates selective transport of the opposite ionic species and generates a net ionic current whose sign and magnitude are set by the charge-geometry alignment. Further investigating the ionic transport behavior shows that peak charge selectivity is achieved at near-complete electric double layer overlap and at a pressure gradient just below the Regime I–Regime II threshold. Random walk particle tracking confirms selective rectification and quantifies the dependence of ion dispersion on surface charge placement across both regimes.