We investigated how allochthonous and autochthonous sources of dissolved organic matter (DOM) affected the optical conditions and chemical characteristics of two contrasting tropical freshwater systems (Dom Helvécio-DH and Pampulha reservoir) in a dry and rainy period in 2013. We analyzed PAR (photosynthetically active radiation) and UV (ultraviolet) attenuation coefficients, nutrients, chlorophyll-a (Chl-a), dissolved organic matter (DOC) and spectral characteristics of CDOM (colored dissolved organic matter). Significant differences in CDOM sources and quantity were observed, with a dominantly terrestrial input in DH during the rainy period with approximately 50% higher DOC and Chl-a levels, and a doubling in total nitrogen (TN) and total phosphorus (TP) compared to the dry winter period. The eutrophic Pampulha had several fold higher levels of DOC, Chl-a, TN and TP, with organic matter of mostly originating from phytoplankton in both seasons. Differences in source and quantity had strong implications on water transparency, DOC concentrations, CDOM quality and its susceptibility to photo- and biodegradation. DH was several fold clearer in both the UV and PAR spectrum. In DH transparency to both UV and PAR radiation was highest during the summer, suggesting elevated photo- and biodegradation during stratification. Pampulha was most transparent in the dry period even during period of algal bloom. In both systems we observed seasonal variations in concentrations of nutrients and Chl-a, and in DH differences were also found in DOC concentrations as well as the specific UV absorbance (SUVA254) and molecular size (M). Our results documents that different sources of DOM and seasonal inputs reflect in the seasonality of apparent and inherent optical properties and nutrients availability with implications for water quality and aquatic community.