Natural organic matter (NOM) in drinking water can react with disinfectants to form disinfection by-products (DBPs). Halogenated furanones are a group of emerging DBPs that can account for 20–60% of the total mutagenicity observed in drinking water. This study examined the impacts of bench-scale coagulation and subsequent chlorination on DBP formation as well as genotoxicity using three source waters located in Ontario, Canada. Two halogenated furanones 3-chloro-4-(dichloromethyl)-2(5H)-furanone (MX) and mucochloric acid (MCA) were analyzed; along with trihalomethanes (THMs), haloacetic acids (HAAs), and absorbable organic halides (AOX). NOM was quantified using liquid chromatography–organic carbon detection (LC–OCD). Measured MX and MCA formation was 6.9–15.3 ng/L and 43.2–315 ng/L following optimized coagulation and subsequent chlorination of the three waters tested. DBP formation and speciation were evaluated as a function of the specific NOM fractions present in the source waters. Humics, building blocks, and biopolymers were highly correlated with DBP formation. Correlations between DBPs were also investigated and a potential relationship between MCA and/or MX vs. HAAs was observed. MX was the only measured DBP that contributed to genotoxicity, representing less than 0.001% of AOX by mass but responsible for 40–67% of the genotoxic response in chlorinated Ottawa River water samples. Genotoxic potential decreased with alum dosages, signifying that coagulation was effective at removing genotoxic DBP precursors.