We would like to thank Jackie Hurst for her help in constructing the figures and three anonymous reviewers for their constructive comments that helped improve the manuscript. This work was funded by the Fonds de Recherche sur la Nature et les Technologies of Québec, the U.S. Office of Naval Research, the Natural Sciences and Engineering Research Council of Canada, and the Canadian Foundation for Climate and Atmospheric Sciences.
Adcroft, A., , Hill C. , , and Marshall J. , 1997: Representation of topography by shaved cells in a height coordinate ocean model. Mon. Wea. Rev, 125 , 2293–2315.
Afanasyev, Y. D., , and Peltier W. R. , 2001: On the breaking internal waves over the skill in Knight Inlet. Proc. Roy. Soc. London, A457 , 2799–2825.
Arakawa, A., 1966: Computational design for long-term numerical integration of the equations of fluid motion: Two-dimensional incompressible flow. Part I. J. Comput. Phys, 1 , 119–143.
Armi, L., , and Farmer D. , 1986: Maximal two-layer exchange through a contraction with barotropic net flow. J. Fluid Mech, 164 , 27–51.
Blumberg, A. F., 1977: A two-dimensional numerical model for the simulation of partially mixed estuaries. Estuarine Processes. Volume II: Circulation, Sediments, and Transfer of Material in the Estuary, M. Wiley, Ed., Academic Press, 1–16.
Bogucki, D., , and Garrett C. , 1993: A simple model for shear-induced decay of an internal solitary wave. J. Phys. Oceanogr, 23 , 1767–1776.
Bourgault, D., , and Kelley D. E. , 2003: Wave-induced boundary mixing in a partially mixed estuary. J. Mar. Res, 61 , 553–576.
Chapman, D. C., 1985: Numerical treatment of cross-shelf open boundaries in a barotropic coastal ocean model. J. Phys. Oceanogr, 15 , 1060–1075.
Cummins, P. F., 2000: Stratified flow over topography: Time-dependent comparisons between model solutions and observations. Dyn. Atmos. Oceans, 33 , 43–72.
Cummins, P. F., , Vagle S. , , Armi L. , , and Farmer D. M. , 2003: Stratified flow over topography: Upstream influence and generation of nonlinear internal waves. Proc. Roy. Soc. London, A459 , 1467–1487.
Farmer, D. M., , and Freeland H. , 1983: The physical oceanography of fjords. Progress in Oceanography, Vol. 12, Pergamon, 147–220.
Farmer, D. M., , and Armi L. , 1986: Maximal two-layer exchange over a sill and through the combination of a sill and contraction with barotropic flow. J. Fluid Mech, 164 , 53–76.
Farmer, D. M., , and Armi L. , 1999a: The generation and trapping of internal solitary waves over topography. Science, 283 , 188–190.
Farmer, D. M., , and Armi L. , 1999b: Stratified flow over topography: The role of small-scale entrainment and mixing in flow establishment. Proc. Roy. Soc. London, A455 , 3221–3258.
Ford, M., , Wang J. , , and Cheng R. T. , 1990: Predicting the vertical structure of tidal current and salinity in San Francisco Bay, California. Water Resour. Res, 26 , 1027–1045.
Geyer, W. R., , and Smith J. D. , 1987: Shear instability in a highly stratified estuary. J. Phys. Oceanogr, 17 , 1668–1679.
Gillibrand, P. A., , Turrell W. R. , , and Elliott A. J. , 1995: Deep-water renewal in the upper basin of Loch Sunart, a Scottish fjord. J. Phys. Oceanogr, 25 , 1488–1503.
Hamilton, P., 1975: A numerical model of the vertical circulation of tidal estuaries and its application to the Rottardam waterway. Geophys. J. Roy. Astron. Soc, 40 , 1–21.
Hibiya, T., , Niwa Y. , , and Fujiwara K. , 1998: Numerical experiments of nonlinear energy transfer within the oceanic internal wave spectrum. J. Geophys. Res, 103 (C9) 18715–18722.
Klymak, J. M., , and Gregg M. C. , 2001: The three-dimensional nature of flow near a sill. J. Geophys. Res, 106 , 22295–22311.
Klymak, J. M., , and Gregg M. C. , 2003: The role of upstream waves and a downstream density pool in the growth of lee waves: Stratified flow over the Knight Inlet sill. J. Phys. Oceanogr, 33 , 1446–1461.
Lamb, K. G., 1994: Numerical experiments of internal wave generation by strong tidal flow across a finite amplitude bank edge. J. Geophys. Res, 99 , 843–864.
Lane-Serff, G. F., , Smeed D. A. , , and Postlethwaite C. R. , 2000: Multi-layer hydraulic exchange flows. J. Fluid Mech, 416 , 269–296.
Lavelle, J. W., , Cokelet E. D. , , and Cannon G. A. , 1991: A model study of density intrusions into and circulation within a deep, silled estuary: Puget Sound. J. Geophys. Res, 96 (C9) 16779–16800.
Lee, C-Y., , and Beardsley R. C. , 1974: The generation of long nonlinear internal waves in a weakly stratified shear flow. J. Geophys. Res, 79 , 453–462.
Lu, Y., , Wright D. G. , , and Brickman D. , 2001: Internal tide generation over topography: Experiments with a free-surface z-level ocean model. J. Atmos. Oceanic Technol, 18 , 1076–1091.
Marshall, J., , Adcroft A. , , Hill C. , , Perelman L. , , and Heisey C. , 1997a: A finite-volume, incompressible Navier Stokes model for studies of the ocean on parallel computers. J. Geophys. Res, 102 (C3) 5753–5766.
Marshall, J., , Hill C. , , Perelman L. , , and Adcroft A. , 1997b: Hydrostatic, quasi-hydrostatic, and nonhydrostatic ocean modelling. J. Geophys. Res, 102 (C3) 5733–5752.
Michallet, H., , and Ivey G. N. , 1999: Experiments on mixing due to internal solitary waves breaking on uniform slopes. J. Geophys. Res, 104 (C6) 13467–13477.
Pacanowski, R. C., , and Philander S. G. H. , 1981: Parameterization of vertical mixing in numerical models of the tropical oceans. J. Phys. Oceanogr, 11 , 1443–1451.
Pietrzak, J., 1998: The use of TVD limiters for forward-in-time upstream-biased advection schemes in ocean modeling. Mon. Wea. Rev, 126 , 812–830.
Porté-Agel, F., , Meneveau C. , , and Parlange M. B. , 2000: A scale-dependent dynamic model for large-eddy simulation: Application to a neutral atmospheric boundary layer. J. Fluid Mech, 415 , 261–284.
Press, W., , Teukolsky S. , , Vetterling W. , , and Flannery B. , 1992: Numerical Recipes in FORTRAN: The Art of Scientific Computing. 2d ed. Cambridge University Press, 963 pp.
Smagorinsky, J., 1963: General circulation experiments with primitive equations. I. The basic experiment. Mon. Wea. Rev, 91 , 99–164.
Stacey, M. W., , Pond S. , , and Nowak Z. P. , 1995: A numerical model of the circulation in Knight Inlet, British Columbia, Canada. J. Phys. Oceanogr, 25 , 1037–1062.
Wang, D-P., , and Kravitz D. W. , 1980: A semi-implicit two-dimensional model of estuarine circulation. J. Phys. Oceanogr, 10 , 441–454.
Wang, J., 1998: A two-channel laterally averaged estuarine circulation model (laecim). J. Geophys. Res, 103 (C9) 18381–18391.
Winters, K. B., , and Seim H. E. , 2000: The role of dissipation and mixing in exchange flow through a contracting channel. J. Fluid Mech, 407 , 265–290.