In this paper, we describe a numerical model to simulate the evolution in time of the hydrodynamics of water storage tanks, with particular emphasis on the time evolution of chlorine concentration. The mathematical model contains several ingredients particularly designed for this problem, namely, a boundary condition to model falling jets on free surfaces, an arbitrary Lagrangian-Eulerian formulation to account for the motion of the free surface because of demand and supply of water, and a coupling of the hydrodynamics with a convection-diffusion-reaction equation modeling the time evolution of chlorine. From the numerical point of view, the equations resulting from the mathematical model are approximated using a finite element formulation, with linear continuous interpolations on tetrahedra for all the unknowns. To make it possible, and also to be able to deal with convection-dominated flows, a stabilized formulation is used. In order to capture the sharp gradients present in the chlorine concentration, particularly near the injection zone, a discontinuity capturing technique is employed. Copyright (c) 2015John Wiley & Sons, Ltd.