Modeling tidal circulation and stratification in Skagit River estuary using an unstructured grid ocean model Zhaoqing Yang * , Tarang Khangaonkar Battelle Marine Sciences Laboratory, 1100 Dexter Avenue North, Suite 400, Seattle, WA 98109, USA article info Article history: Received 19 April 2008 Received in revised form 12 July 2008 Accepted 21 July 2008 Available online 29 July 2008 Keywords: Unstructured Mesh Estuary Tidal flats Tidal Circulation Salinity Intrusion abstract Tidal circulation and river plume dynamics in shallow-water estuarine systems with large intertidal zones are complex. Strong asymmetries in tidal currents and stratification often occur in the intertidal zones and subtidal channels over a tidal cycle. The Skagit River is the largest estuary with respect to the discharge of a significant amount of freshwater and sediment into Puget Sound, Washington. It con- sists of a large intertidal zone with multiple tidal channels near the mouth of the estuary. To simulate the tidal circulation and salinity stratification accurately in the intertidal region, an unstructured grid numer- ical model with wetting–drying capability and the capability to accurately represent the bathymetry of tidal flats and the geometry of shallow distributary channels is necessary. In this paper, a modeling study for the Skagit River estuary using a three-dimensional unstructured grid, finite-volume coastal ocean model (FVCOM) supported by high-resolution LIDAR data is presented. The hydrodynamic model was validated with observed water surface elevation, velocity, and salinity data over spring and neap tidal cycles under low-river-flow and high-river-flow conditions. Wetting and drying processes in the inter- tidal zone and strong stratification in the estuary were simulated successfully by the model. Model results indicate that the Skagit River estuary is a highly stratified estuary, but destratification can occur during flood tide. Tides and baroclinic motion are the dominant forcing in the Skagit River estuary, but strong wind events can affect the currents in the intertidal zone significantly. Preliminary analysis also indicated that the salinity intrusion length scale is proportional to the river flow to the  1 = 4 power. Ó 2008 Elsevier Ltd. All rights reserved. 1. Introduction Intertidal zones of estuaries with large tidal flats play an impor- tant role on tidal circulation, salinity intrusion, and sediment transport. Intertidal zones often include different marine habitats that support a wide variety of marine species. The long-term sta- bility and sustainability of these habitats is threatened by growing anthropogenic pressures and from potential changes brought about by climate change and sea level rise. Tidal circulation and salinity intrusion processes in intertidal regions generally are very complex and highly dynamic due to the effect of extreme shallow water depths in the tidal flats and tidal channels. This complexity is illustrated, for instance, by asymmetry of vertical mixing be- tween ebb and flood currents, and dispersion of salinity gradients due to lateral advection over the intertidal zone (Geyer et al., 2000; Ralston and Stacey, 2005). Complexities can also arise be- cause during low tides, some of the channels may be blocked, resulting in ponding of water, occurrence of transient shallow wave induced currents, and wind effects (Greenberg et al., 2005; Gorman and Neilson, 1999; Collins et al., 1998). However, because of difficulties in conducting undisturbed field measurements, the lack of high-resolution bathymetric and topographic data, and computational limitations with simulation of wetting and drying process, the intertidal zone has not received much attention, and circulation processes are not understood as well. In recent years, some advanced numerical models have been developed for coastal oceans and estuaries with improved perfor- mance, including the capability of simulating wetting and drying process (Zhang et al., 2004; Ji et al., 2001; Chen et al., 2003; Oey, 2006; Casulli and Zanolli, 1998, 2002; Cheng and Casulli, 2004). Numerical models with an unstructured grid framework (Chen et al., 2003; Zhang et al., 2004; Cheng and Casulli, 2004) and the availability of high-resolution light detection and ranging (LI- DAR) data in the tidal flats make it possible to simulate hydrody- namics in estuaries with large tidal flats with satisfactory accuracy. This capability is of considerable value to a large community of biologists, geomorphologists, ecologists, and restoration planners engaged in the activity of restoring tidal estuarine functions and nearshore habitat in support of fish stock recovery as in the case of in Puget Sound, Washington, and other estuarine and coastal regions around United States. In this paper, we present a modeling study of tidal circulation and salt intrusion in a highly stratified 1463-5003/$ - see front matter Ó 2008 Elsevier Ltd. All rights reserved. doi:10.1016/j.ocemod.2008.07.004 * Corresponding author. Tel.: +1 206 528 3056; fax: +1 206 528 3556. E-mail address: zhaoqing.yang@pnl.gov (Z. Yang). Ocean Modelling 28 (2009) 34–49 Contents lists available at ScienceDirect Ocean Modelling journal homepage: www.elsevier.com/locate/ocemod