There is growing concern about the impact of agricultural practices on water quality. The loss of nutrients such as nitrogen and phosphorous through agricultural runoff poses a potential risk of water quality degradation. However, it is unclear how dissolved organic matter (DOM) composition is associated with pollution levels in water bodies. To address this, we conducted a cross-year investigation to reveal the nature of DOM and its relationship to water quality in agricultural effluents (AEs) and livestock effluents (LEs). We discovered that DOM fluorescence components of AEs were mainly from autochthonous and terrestrial sources, while in LEs it was primarily from autochthonous sources. LEs showed a higher β:α and biological index (BIX) than AEs, indicating that LEs had higher biological activity. Compared to the LEs, DOM in AEs exhibited a higher humification index (HIX), illustrating that DOM was more humic and aromatic. Overall, our results suggest that the BIX and fluorescence index (FI) were best suited for the characterization of water bodies impacted by LEs and AEs. Excitation-emission matrix spectroscopy and parallel factor (EEMs-PARAFAC) analysis showed that DOM in AEs was mainly a humic-like material (~64%) and in LEs was mainly protein-like (~68%). Tryptophan-like compounds (C1) were made more abundant in AEs because of the breakdown of aquatic vegetation. The microbial activity enhanced protein-like substances (C1 and C2) in LEs. Our study revealed a positive correlation between five-day biochemical oxygen demand (BOD5) concentrations and tyrosine-like substance components, suggesting that fluorescence peak B may be a good predictor of water quality affected by anthropogenic activities. For both LEs and AEs, our results suggest that peak D may be a reliable water quality surrogate for total phosphorus (TP).