Dissolved organic matter (DOM) is increasing in many drinking water supplies, which can have adverse impacts on treatment. Magnetic ion exchange (MIEX) is an advanced treatment process that has been shown to effectively remove DOM from different water sources. DOM removal efficiency is typically determined through dissolved organic carbon (DOC) and ultraviolet absorbance (UVA) measurements, but these methods can be limited in the amount of information they provide on DOM. Fluorescence spectroscopy has been suggested as a more robust characterization technique for monitoring DOM, but there remain gaps in knowledge between DOM removal processes and fluorescence characterization of DOM. Accordingly, the goal of this research was to evaluate the impact of MIEX treatment on DOM fluorescence for diverse water sources. MIEX jar tests were conducted using surface water, synthetic water, groundwater, and landfill leachate wastewater, and analyzed for DOC, UVA, and fluorescence excitation-emission matrix (EEM). Fluorescence EEMs were used to determine fluorophore location, intensity, and fluorescence index. MIEX removal of DOC and UVA were strongly correlated with MIEX removal of peak fluorescence intensity across all water sources. Peak fluorescence location indicated that MIEX preferentially removed terrestrial DOM. Fluorescence is a promising tool for monitoring DOM removal efficiency by MIEX treatment.