Two Lagrangian water quality models are described. The models are simple and inexpensive to use and simulate the mixing and flushing of wastes in a well-mixed estuary. One model represents the estuary as a series of connected volumes (or boxes) of water which travel up and down the estuary with the tidal water movement. The other model incorporates two layers of boxes traveling up and down the estuary. Since the same volume of water remains within each box, the mixing of waste between adjacent boxes is explicitly modeled. Thus the finite difference equation describing waste mixing in the Lagrangian box model creates very little numerical diffusion and so the effects of waste interaction and decay can also be represented accurately. The two layer model involves a more complicated calculation procedure but provides a more realistic approximation of the dispersion process. The accuracy and stability of the equations used are discussed and the calibration and verification of the models for one harbour are demonstrated.