This paper presents the effects of thermal regeneration of granulated active carbon (GAC) inhabited by microorganisms on the efficiency of dissolved organic matter removal from surface water. The thermal regeneration of the bed ensured a change in the shares of the particular organic matter fractions. The regeneration of GAC resulted in an increase in refractive organic matter removal and in a considerable reduction in biodegradable dissolved organic carbon (BDOC) removal. However, the process of bringing the deposit back to biological activity was found to be long (about four months) and did not ensure the pre-regeneration efficiency of biodegradable dissolved organic carbon removal.