Phase-separated membrane domains, also known as lipid rafts, are believed to play an important role in cell function. Although most rafts are sterol-enriched membrane regions, evidence suggests that living cells may also contain gel-like rafts. Interactions between gel and fluid domains have a large impact on membrane properties, as is the case with permeability. The membrane permeability may reach a peak at the main phase transition temperature, by far exceeding the values recorded at the fluid phase. It has been proposed that gel-fluid interfaces are leaky, but the effect has not yet been demonstrated at the molecular level. Here, we performed atomistic molecular dynamics simulations of phospholipid bilayers with coexisting gel-like and fluid domains. We found that the thickness mismatch between both phases, the membrane elasticity, and the lipid packing acted together to promote the formation of a thickness minimum at the gel-fluid interface. Free energy calculations showed that pore-mediated ionic permeation was strongly facilitated at the constriction region, whereas water permeation by simple diffusion was only marginally affected. Long-lived, peristaltic undulations were recorded at the bulk fluid phase near the main transition temperature. They gave rise to thickness minima that, although shallower than the interface constrictions, could also enhance permeability. Finally, we demonstrated that an interface constriction was also formed at the boundaries of regular, cholesterol-enriched lipid rafts. Our simulation results will hopefully contribute to a better understanding of biological processes such as transport, signaling, and cellular damage promoted by low temperature and dehydration.