Chromophoric Dissolved Organic Matter (CDOM) is an important component in freshwater and marine ecosystems and plays direct and indirect role in biogeochemical cycles. CDOM originates from the degradation process of organic materials, usually macrophytes and planktons. The present work examines the importance of wetland derived CDOM on the optical and bio-optical properties of two bays of Lake Victoria (Uganda, Africa). This was achieved by determining the attenuation and extinction coefficients of filtered and unfiltered water samples from two equatorial bays on the Ugandan coastline of Lake Victoria. Katonga Bay is a wetland lined bay that receives water from the Katonga river, while Bunjako Bay is an outer bay between Katonga Bay and Lake Victoria. The results showed that attenuation was highest in Katonga Bay and the role of CDOM is most dominant near the river inlet. The quantity and quality of CDOM is extremely different in the two bays: in Katonga Bay it is possible to hypothesize a terrestrial origin of CDOM (transported by the wetland river). On the contrary, in Bunjako Bay, spectral measurements of absorption indicate a modified CDOM and/or alternative CDOM source. The terrestrial CDOM in Katonga Bay is more capable of absorbing harmful UV radiation than the CDOM present in the Bunjako Bay. The resulting optical environment in the former bay presented a water column with a very limited penetration of harmful UV radiation, while a higher penetration was observed in the Bunjako Bay.