Many ion channels have remarkably large water-containing spaces (pockets) within the membrane-spanning region of the channel protein. These are often adjacent to a selectivity filter. The pockets are unusual since they are often formed by rather hydrophobic protein surfaces. In some cases, de-wetting transitions have been suggested as having roles in channel gating. Evaluation of the amounts and trans-membrane distribution of water within ion channels can be determined by neutron diffraction from multilayers using D2O/H2O exchange. The main difficulty is the high protein/lipid molar ratios needed in multilayers if water in the channels is to be a accurately measured. We used the M2 peptide of H1N1 influenza virus to form multilayers of high protein content. This peptide forms tetrameric proton channels by self-assembly in lipid bilayers. Protein to lipid molar ratios as high as 1/3 formed good multilayers for neutron diffraction. We obtained trans-membrane water distributions using the AND/R instrument at the NIST Center for Neutron Research. Neutron diffraction data for three lamellar orders were obtained and Fourier D2O/H2O difference profiles show considerable water penetration into the membrane, consistent with water approaching the selectivity filter. The M2 channel water profile is strikingly different from that of the lipid-only membrane, which has a profile that is flat in the hydrocarbon region. For further comparison, the water profile obtained for purple membranes, which are of similar high protein content, is also presented and shows little water in the hydrocarbon region. Aspects of water in hydrophobic pockets are discussed.