In this manuscript, we provide a general theory for how surface phonons couple to molecular adsorbates. Our theory maps the extended dynamics of a surface's atomic vibrational motions to a generalized Langevin equation, and by doing so captures these dynamics in a single quantity: the non-Markovian friction. The different frequency components of this friction are the phonon modes of the surface slab weighted by their coupling to the adsorbate degrees of freedom. Using this formalism, we demonstrate that physisorbed species couple primarily to acoustic phonons while chemisorbed species couple to dispersionless local vibrations. We subsequently derive equations for phonon-adjusted reaction rates using transition state theory and demonstrate that these corrections improve agreement with experimental results for CO desorption rates from Pt(111).