Under certain conditions morphology changes occur when thin Pd films, grown on SiO2 at room temperature, are subject to elevated temperatures. First holes in the metal are observed, followed by network formation and finally isolation of metal islands. This process is known as agglomeration. The influence of gas exposures on this restructuring process has been studied by following variations in the capacitance of the structure and by atomic force microscopy, transmission electron microscopy and ultraviolet photoelectron spectroscopy. The capacitance measurements show that carbonaceous species have an impeding influence on the rate of agglomeration and may lock the film structure in a thermodynamic non-equilibrium state. By removing these species with oxygen exposure, i.e. by forming volatile CO and CO2, a clean surface is obtained and the agglomeration process can proceed. High oxygen or hydrogen coverages also lower the rate of restructuring, compared to the case of a clean surface. For the clean Pd surface, an apparent activation energy of 0.64 eV is found for the restructuring process.