Effluent organic matter (EfOM) is a key precursor of disinfection byproducts (DBPs), posing major challenges to the safe reuse of treated wastewater. However, the molecular composition and chlorine reactivity of EfOM are expected to differ substantially across industrial and municipal sources, yet their impacts on DBP formation and toxicity remain unclear. Here, effluents from 17 sources, representing electronic, pharmaceutical, food, hospital, and municipal sewage wastewaters, were characterized using spectrofluoroscopy and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), coupled with chlorination and bioassay experiments. Compared to sewage EfOM, pharmaceutical, food, and hospital wastewater EfOM showed comparable aromaticity, molecular size, and DBP yields and toxicity after chlorination. However, electronic wastewater EfOM exhibited much lower aromaticity and higher proportions of protein- and lipid-like compounds, resulting in lower trihalomethane and haloacetonitrile yields and lower cytotoxic DBP mixture after chlorination. Molecular formulas such as C17H34O5, C13H20O11, C23H32O7S, C12H24O4, and C14H20O3S were unique to electronic, pharmaceutical, food, hospital, and sewage wastewaters in FT-ICR MS analysis, suggesting their potential as source-specific molecular markers. Although the trihalomethane yield correlated with organic matter aromaticity as previously reported, the relations between other DBP yields and organic matter characteristics differed from those reported for natural organic matter, suggesting different chlorine reactivity of EfOM from that of natural organic matter. These findings establish a molecular basis linking EfOM composition to DBP formation and toxicity, highlighting the need for source-specific risk assessment and control strategies in wastewater reuse management.