This study aims to investigate the influence of the coexistence of halogen ions (bromide/iodide) and biological source matters on the speciation and yield of trihalomethanes (THMs), haloacetic acids (HAAs), and N-nitrosodimethylamine (NDMA) during the ozonation and subsequent chlorination of water. The results show that the concentrations of brominated THMs and iodinated THMs increased with increasing bromide and iodide concentration. These results may be attributed to the higher reactivity of hypobromous acid and hypoiodous acid generated from the ozonation and subsequent chlorination in the presence of bromide or iodide ions. The presence of bromide increased the species of brominated HAAs. There was a shift from chlorinated HAAs to brominated HAAs after increasing the concentration of bromide. The effect of iodide on HAA formation was more complex than bromide. For most samples, the concentration of total HAAs (T-HAAs) increased to the maximum and then decreased with increasing iodide concentration. The components of the organic precursors also significantly influenced the formation of brominated and iodinated disinfection by-products (Br-DBPs and I-DBPs). Humic acids produced more CHBr3 (596.60 μg/L) than other organic materials. Microcystis aeruginosa cells produced the most tribromoacetic acid (TBAA, 84.16 μg/L). Furthermore, the yield of NDMA decreased with increasing bromide concentration, indicating that the formation of NDMA was inhibited by the high concentration of bromide.