Degradation of the photocathode materials employed in photoinjectors represents a challenge for sustained operation of nuclear physics accelerators and high power free electron lasers (FEL). Photocathode quantum efficiency degradation is due to residual gases in the electron source vacuum system being ionized and accelerated back to the photocathode. These investigations are a first attempt to characterize the nature of the photocathode degradation, and employ multiple surface and bulk analysis techniques to investigate damage mechanisms including sputtering of the Cs-oxidant surface monolayer, other surface chemistry effects, and ion implantation. Surface and bulk analysis studies were conducted on two GaAs photocathodes, which were removed from the JLab FEL DC photoemission gun after delivering electron beam, and two control samples. The analysis techniques include helium ion microscopy, Rutherford backscattering spectrometry (RBS), atomic force microscopy, and secondary ion mass spectrometry (SIMS). In addition, two high-polarization strained superlattice GaAs photocathode samples, one removed from the continuous electron beam accelerator facility (CEBAF) photoinjector and one unused, were also analyzed using transmission electron microscopy (TEM) and SIMS. It was found that heat cleaning the FEL GaAs wafer introduces surface roughness, which seems to be reduced by prolonged use. The bulk GaAs samples retained a fairly well organized crystalline structure after delivering beam but show evidence of Cs depletion on the surface. Within the precision of the SIMS and RBS measurements, the data showed no indication of hydrogen implantation or lattice damage from ion back bombardment in the bulk GaAs wafers. In contrast, SIMS and TEM measurements of the strained superlattice photocathode show clear crystal damage in the wafer from ion back bombardment.