Functionalized nanoparticles (NPs) are considered suitable carriers for targeted drug delivery systems. However, the ion and water leakage induced by permeation of these nanoparticles is a challenge in these drug delivery methods because of cytotoxic effects of some ions. In this study, we have carried out a series of coarse-grained molecular dynamics simulations to investigate the effect of length of ligands on permeation of a nanoparticle across a protein-free phospholipid bilayer membrane. Water and ion penetration as well as incidence of lipid flip-flop events and loss of lipid molecules from the membrane are explored in this study while varying the nanoparticle size, length of ligand, ion concentration gradient, pressure differential across the membrane, and nanoparticle permeation velocity. Some results from our studies include (1) the number of water molecules in the interior of the membrane during ligand-coated nanoparticle permeation increases with nanoparticle size, ligand length, pressure differential, and permeation velocity but is not sensitive to the ion concentration gradient; (2) some lipid molecules leave the membrane by being entangled with ligands of the NP instead of completing the flip-flop that permits them to rejoin the membrane, thereby leading to fewer flip-flop events; and (3) the formation of water columns or water fingers provides a mechanism of ion transport across lipid bilayer membranes, but such ion penetration events are less likely for sodium ions than chloride ions and less likely for nanoparticles with longer-ligands.