With X-ray and neutron reflectivity, the structure and composition of polyelectrolyte multilayers from poly(allyl amine) (PAH) and poly(styrene sulfonate) (PSS) are studied as function of preparation conditions (salt concentration and solution temperature, T). The onset of a temperature effect occurs at 0.05 M NaCl (Debye length similar to 1 nm). At 1 M salt, the film thickness increases by a factor of 3 on heating the deposition solution from 5 to 60 degrees C. The PAH/PSS bilayer thickness is independent of the kind of salt (NaCl or KCl), yet its composition is different (more bound water for NaCl). At low T, the internal roughness is 33% of the bilayer thickness; it increases to 60% at high T. The roughening is accompanied by a total loss of bound water. At which temperature the roughening starts is a function of the kind of salt (50 degrees C for NaCl and 35 degrees C for KCl). The strong temperature dependence and the eventual loss of bound water molecules may be attributed to the hydrophobic force; however, there is an isotope effect, since the loss of bound water is less pronounced in the deuterated layers.