Using a laboratory-scale system, consisting of a primary disinfection tank (PDT) and three intermittently mixed reactors (R1–R3) in series, bulk water and biofilm contributions to chlorine decay were quantified. The reactors (surface-to-volume ratio: 23.7 m⁻¹; retention time in each reactor: 42.6 ± 1.18 h) were fed with plant-filtered water (PFW). Secondary disinfection was carried out in R1. Free chlorine concentration decreased with travel time (R1: 1.2 mg/L; R2: 0.6 mg/L; and R3: 0.12 mg/L). The bacterial number (ATP) decreased from 67 pg/mL in PFW and remained at ~2–3 pg/mL in R1 and R2 but increased back to 68 pg/mL in R3. First-order chlorine decay rate coefficients decreased from R1 to R2, as expected, but increased by five-fold from R2 to R3. The increased bacterial number (ATP) in R3 and batch chlorine decay tests confirmed that bulk water (soluble compounds, microbes, and sediments) contributed approximately 40% of the decay, and the biofilm contributed 60% in R3. When ATP levels in the reactors were combined with literature data, the bacterial number increased significantly when free chlorine decreased below 0.2 mg/L, but data between 0.2 and 0.5 mg/L are limited. More investigation is needed in the future for chlorine < 0.5 mg/L regarding bacterial regrowth and its effect on bulk water chlorine decay.