Photo-cross-linkable polyelectrolyte multilayers were made from poly(allylamine) (PAH) and poly(acrylic acid) (PAA) modified with a photosensitive benzophenone. Nanoindentation, using atomic force microscopy (AFM) of these and unmodified PAH/PAA multilayers, was used to assess their mechanical properties in situ under an aqueous buffer. Under the conditions employed (and a 20 nm radius AFM tip), reliable nanoindentations that appeared to be decoupled from the properties of the silicon substrate were obtained for films greater than 150 nm in thickness. A strong difference in the apparent modulus was observed for films terminated with positive as compared to negative polyelectrolytes. Films terminated with PAA were more glassy, suggesting better charge matching of polyelectrolytes. Multilayers irradiated for up to 100 min showed a smooth controlled increase in the modulus with little change in the water contact angle. The permeability to iodide ion, measured electrochemically, also decreased in a controlled fashion.