Disinfection by-products (DBPs) are an ever-increasing occurrence in water networks, particularly those which abstract water from peatland areas. Although much research has been carried out to discover novel methods to remove specific DBPs, the removal of natural organic matter (NOM) from source water may provide a more sustainable solution in many areas. This study focuses on the removal of NOM by novel filters, which could be retrospectively fitted to any conventional water treatment facility. The filters comprised stratified layers of a variety of media, including sand, Bayer residue, granular activated carbon (GAC), and pyritic fill. The filters were operated under two loading regimes, continuous and intermittent, at loading rates similar to recognised design standards. The most successful filter design comprised stratified layers of sand, GAC, and pyritic fill. Over the duration of a 240 day study, these filters obtained average dissolved organic carbon removal rates of 40%, and achieved average specific ultra-violet absorbance reductions from 2.9 to 2.4 L mg−1 m−1. The study demonstrates that these novel filters may be used to reduce NOM levels, thus reducing the potential for DBP formation. Such designs can incorporate the use of waste media, making the overall design more sustainable and robust.