Effective disinfection is essential for maintaining water quality standards in distribution networks. Chlorination, as the most used technique, ensures safe water by maintaining sufficient chlorine residuals but also leads to the formation of disinfection byproducts (DBPs). These DBPs pose health risks, highlighting the need for chlorine injection control (CIC) by booster stations to balance safety and DBPs formation. Prior studies have followed various approaches to address this research problem. However, most of these studies overlook the changing flow conditions and their influence on the evolution of the chlorine and DBPs concentrations by integrating simplified transport-reaction models into CIC. In contrast, this paper proposes a novel CIC method that: (i) integrates multi-species dynamics, (ii) allows for a more accurate representation of the reaction dynamics of chlorine, other substances, and the resulting DBPs formation, and (iii) optimizes for the regulation of chlorine concentrations subject to EPA mandates thereby mitigating network-wide DBPs formation. The novelty of this study lies in its incorporation of time-dependent controllability analysis that captures the control coverage of each booster station. The effectiveness of the proposed CIC method is demonstrated through its application and validation via numerical case studies on different water networks with varying scales, initial conditions, and parameters.