Studies were carried out to assess changes in biodegradable dissolved organic carbon (BDOC) and assimilable organic carbon (AOC) in groundwater and surface waters after two processes: ozonation and ozonation/UV. The tested water was in contact with O3 firstly for 4 and secondly for 15 min. Three doses of disinfectant were used: 1.6 mg/L, 5.0 mg/L, and 10.0 mg/L. The UV radiation time was 10 and 30 min. The greatest change in AOC and BDOC for groundwater was observed at an O3 dose of 10.0 mg/L and a contact time of 15 min, by 400 and 197%, respectively. On the other hand, for surface water, it was shown that after the ozonation/UV process, the AOC and BDOC content decreased after both 10 and 30 min of radiation in comparison to the water after ozonation. The AOC content decreased by 33% and 22%, respectively, and the BDOC content by 27% and 31%, respectively. The results obtained in this study provide new information on the effect of different ozonation conditions and the combined method on the level of biodegradable organic fraction of water. It is recommended that BDOC and AOC should be monitored in Poland as routine indicators during the preparation of drinking water.