The influence of microwave radiation (2.45 GHz, 1.5 W/cm2, up to 80 s) on defects was studied in single crystals of n-6H–SiC, n-GaAs, and epi-GaAs. The capture cross section of the charge carrier was found to change, and defect complexes were reconstructed because of the growing number of interstitial atoms in the near-surface layer. The correlation between the changes in the defect subsystem and deformation of the near-surface layer was analyzed. The possible mechanisms of the revealed effects are also discussed.