Rivers act as carriers where active cycling of chromophoric dissolved organic matter (CDOM) affected by anthropogenic activities and land cover variation may occur. Little is known about the optical properties of CDOM in relation to antibiotics; these properties could provide valuable insights into CDOM transformation processes and biogeochemical reactivity. The spatial distribution of CDOM absorption, fluorescence intensities of CDOM components, and correlations between fluorescence indices (FI370, humification index (HIX)) and biological index (BIX)) with water quality and antibiotics were investigated in three rivers, namely, two rivers (Yalu River and Tumen River) dividing China and North Korea, and the Songhua River. Four humic-like components (C1 and C3-5), and one tryptophan-like component (C2), were identified via fluorescence excitation-emission matrices-parallel factor analysis (EEM-PARAFAC). The correlation between Fmax for five EEM-PARAFAC extracted CDOM components, C1-C5, FI370, HIX, BIX, and water quality parameters, and four antibiotics (i.e., Norfloxacin, Enrofloxacin, Sulfamethoxazole and Metronidazole), were determined through a redundancy analysis (RDA), with species-environment correlations of 0.887 and 0.833, respectively. The results showed that spatial variation in land cover, pollution sources, and terrestrial contribution in water quality affected Fmax for the fluorescent components C1-C5 and the fluorescence indices, indicating a high diverse chemical composition and transformation history. The Fmax for terrestrial humic-like components, C4 and C5, showed spatial variation depending on land cover and anthropogenic impacts. Further correlation and regression analyses indicated that CDOM soil fulvic-like component C5 correlated with Sulfamethoxazole and Metronidazole (t test, p < 0.01). Our results indicate that the spatial distributions of Fmax for CDOM fluorescent terrestrial components, evaluated by EEM-PARAFAC, have potential implications for the monitoring of Sulfamethoxazole and Metronidazole in surface waters. Further, these findings can be used to understand the biogeochemical cycling of CDOM and its effects on antibiotics pollution in the environment.