Quinolinium based Cl- sensitive fluorescent indicators have been used extensively to measure intracellular Cl- activity. To define their fluorescence quenching mechanism, a series of N-methyl quinolinium derivatives were synthesized, including N-methylquinolinium (Q), 6-methylQ, 6-methoxyQ, 6-chloroQ, 3-bromoQ, 6-aminoQ and N-methylisoquinolinium. Stern-Volmer plots for quenching by Cl-, Br-, SCN-, I-, F-, OAc- and CO3(2-) from both intensity and lifetime measurements were linear. Bimolecular quenching rate constants (kq) decreased with increasing anion oxidation potentials and increased with increasing quinolinium reduction potentials. The free energy change for charge transfer (deltaG), calculated from indicator spectral and electrochemical properties, was found to correlate with log kq. These results suggest that quenching of quinolinium fluorescence in water by anions involves a charge-transfer quenching mechanism. Understanding the mechanism facilitates structure-based predictions of the anion sensitivities of quinolinium indicators to design improved Cl- indicators with tailored properties.