Water transport through very narrow channels occurs according to the single file mechanism. While entering the channel, every water molecule loses most of its neighbouring water molecules. The energetic costs are thought to be compensated, at least in part, by interactions with the channel wall and by interactions with the lipid headgroups at the channel mouth. Consequently, differences in single channel permeability (pf) measured for gramicidin A channels embedded into different lipids were interpreted in terms of differences in water dehydration costs. However, recent atomistic molecular dynamics simulations identified lipid headgroup interactions with the channel entrance leading to transient blocking of the channel. This observation suggests that the lipid environment affects the channel not only by changing the water energetics but also by mechanically blocking the entrance. To test this hypothesis we measured ion and water fluxes through acylated gramicidin-A derivatives, which were reconstituted into solvent free diphytanoyl-phosphatidyl-choline membranes. Ion conductance of channels with C9 and C10 acyl-chain anchors differed only by about 20 % from wild type gramicidin-A conductance. Similarly, the anchor had only a minor effect on dimer stability as indicated by a decrease in channel lifetime from 2.3 s to 2 s or 1.6 s for the C9 and C10 derivatives, respectively. As the gramicidin channels most of the time do not contain ions, the acyl-chain anchor affects water transport more efficiently. Two C9 anchors increased pf by a factor 2 or 3 depending on their position. In contrast, derivates with only one C9 or C10 acyl anchor showed no increase in pf. Taken together with data about the lipid dependency of pf, these results indicate that the lipid headgroups affect single file transport by both changing the solvation energy and by blocking the channel entrance.