Janus, or two-sided,\ncharged membranes offer promise as ionic current\nrectifiers. In such systems, pores consisting of two regions of opposite\ncharge can be used to generate a current from a gradient in salinity.\nThe efficiency of nanoscale Janus pores increases dramatically as\ntheir diameter becomes smaller. However, little is known about the\nunderlying transport processes, particularly under experimentally\naccessible conditions. In this work, we examine the molecular basis\nfor rectification in Janus nanopores using an applied electric field.\nMolecular simulations with explicit water and ions are used to examine\nthe structure and dynamics of all molecular species in aqueous electrolyte\nsolutions. For several macroscopic observables, the results of such\nsimulations are consistent with experimental observations on asymmetric\nmembranes. Our analysis reveals a number of previously unknown features,\nincluding a pronounced local reorientation of water molecules in the\npores, and a segregation of ionic species that had not been anticipated\nby previously reported continuum analyses of Janus pores. Using these\ninsights, a model is proposed for ionic current rectification in which\nelectric leakage at the pore entrance controls net transport.