Disinfection by-products (DBPs) are potentially toxic compounds formed upon chemical disinfection of drinking water. Controlling the levels and characteristics of dissolved organic matter (DOM) as precursor material for DBPs is a major target to reduce DBP formation. A pilot-scale treatment including suspended ion exchange (SIX (R)), a ceramic microfilter (CeraMac (R)) with in-line coagulation and optional pre-ozonation followed by granular activated carbon (GAC) filtration was compared with a conventional full-scale treatment based on DOM removal and DBP formation using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), rapid fractionation, liquid chromatography organic carbon detection (LC-OCD), adsorbable organic halogens (AOX) and trihalomethane (THM) analysis. The new treatment combination showed different selectivity for DOM removal, compared to the conventional, leading to changes in composition of the DBPs formed. SIX (R) and GAC had the largest impacts on reducing AOX and THM formation potentials but the high adsorptive capacity of GAC affected the diversity of detected DBPs most. Chlorination and chloramination of pilot treated water with doses normally used in Sweden produced low levels of AOX compared to the full-scale treatment, but FT-ICR MS revealed an abundance of brominated DBP species in contrast with the conventional treatment, which were dominated by chlorinated DBPs. This finding was largely linked to the high DOM removal by the pilot treatment, causing an increased Br-/C ratio and a higher formation of HOBr. Potential increases in Br-DBPs are important to consider in minimizing health risks associated with DBPs, because of the supposed higher toxicity of Br-DBPs compared to Cl-DBPs.