A homogeneous distribution of the residual chlorine in secondary water supply tanks guarantees the microbiological safety of drinking water. However, the hydrodynamic conditions and spatiotemporal variations in chlorine are not thoroughly understood, which is attributed to the complicated tank structures and operation modes. In this study, an integrated tank model was developed based on a three-dimensional computational fluid dynamics (CFD) method and variable reaction rate coefficient chlorine decay model. The CFD method was validated by tracking the water levels of the tanks under different operating modes. By combining the hydrodynamic results and chlorine decay model, the effluent chlorine concentrations of two connected tanks—underground and roof-level tanks—were simulated. The tank model was able to achieve good agreement between the predicted and measured effluent concentrations. A comparison of the chlorine concentration and flow velocity profiles confirmed that the hydraulic behavior affected the spatial distribution of chlorine. The results further revealed that the inlet momentum dominated the hydrodynamics of the tanks. The inlet and outlet locations, orientations, and inflow velocities were critical factors for maintaining the residual chlorine concentration in the tanks. With an increase in water depth, the mean residence time distribution had an important role in chlorine consumption.