It has been known since the early 1970s that the application of disinfectants, especially chlorine, results in the formation of disinfection by-products (DBPs), most of which contain covalently bound chlorine, bromine, or iodine. These are known as the halogenated DBPs and they can be measured by a non-specific analytical method know as TOX. Despite nearly three decades of research there still remains a large fraction of DBPs that have not been identified. By comparing the TOX values with the halides attributed to known identifiable by-products (trihalomethanes [THMs], haloacetic acids [HAAs], etc.) we can estimate the unknown TOX (abbreviated here as UTOX) and better understand the formation of these unknown compounds. The objectives of this research were to (1) determine the nature and chemical characteristics of the unknown fraction of the total organic halogen (UTOX) produced during chlorination and alternative disinfection processes (i.e., chloramination, chlorine dioxide, ozone disinfection); (2) assess the impact of treatment on removal of UTOX precursors; and (3) determine the best total organic halide (TOX) protocol to use with ion chromatography (IC) analysis for the purposes of discriminating between total organic chlorine (TOCl), total organic bromine (TOBr), and total organic iodine (TOI). It was found that TOCl, TOBr, and TOI can be accurately and rapidly measured with conventional TOX instruments and an ion chromatograph. Iodide is rapidly oxidized to active iodine under a variety of treatment scenarios, and this leads to large amounts of TOI and measurable amounts of iodinated THMs. However, high levels of free chlorine can over-oxidize the iodide (forming iodate), which does not result in TOI formation. Substantial differences were noted in the tendency for various NOM fractions (hydrophobic, hydrophilic) to form specific classes of DBPs. This behavior was specific to the oxidant such that the major sources of DBP precursors for chlorination were not the same as those observed for chloramination. It was also found that corrosion control compounds can affect DBP distributions and halogen incorporation factors.