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A coupled system of wind, wind wave, and coastal circulation models has been implemented for southern Louisiana and Mississippi to simulate riverine flows, tides, wind waves, and hurricane storm surge in the region. The system combines the NOAA Hurricane Research Division Wind Analysis System (H*WIND) and the Interactive Objective Kinematic Analysis (IOKA) kinematic wind analyses, the Wave Model (WAM) offshore and Steady-State Irregular Wave (STWAVE) nearshore wind wave models, and the Advanced Circulation (ADCIRC) basin to channel-scale unstructured grid circulation model. The system emphasizes a high-resolution (down to 50 m) representation of the geometry, bathymetry, and topography; nonlinear coupling of all processes including wind wave radiation stress-induced set up; and objective specification of frictional parameters based on land-cover databases and commonly used parameters. Riverine flows and tides are validated for no storm conditions, while winds, wind waves, hydrographs, and high water marks are validated for Hurricanes Katrina and Rita.

Transport and dispersion processes in the ocean are crucial, as they determine the lifetime and fate of biological and chemical quantities drifting with ocean currents. Due to the complexity of the coastal ocean environment, numerical circulation models have difficulties to accurately simulate highly turbulent flows and dispersion processes, especially in highly energetic tidal basins such as the eastern English Channel. A method of improving the results of coastal circulation modeling and tracer dispersion in the Dover Strait is proposed. Surface current velocities derived from Lagrangian drifter measurements in November 2020 and May 2021 were optimally interpolated in time and space to constrain a high-resolution coastal circulation MARS model, with careful attention given to selecting ensemble members composing the model covariance matrix. The space–time velocity covariances derived from model simulations were utilized by the optimal interpolation algorithm to determine the most likely evolution of the velocity field under constraints provided by Lagrangian observations and their error statistics. The accuracy of the velocity field reconstruction was evaluated at each time step. The results of the fusion of model outputs with surface drifter velocity measurements show a significant improvement (by ∼ 50 %) of the model capability to simulate the drift of passive tracers in the Dover Strait. Optimized velocity fields were used to quantify the absolute dispersion in the study area. The implications of these results are important, as they can be used to improve existing decision-making support tool or design new tools for monitoring the transport and dispersion in a coastal ocean environment.

In order to protect the diverse ecosystems of coastal California, a series of marine protected areas (MPAs) have been established. The ability of these MPAs to preserve and potentially enhance marine resources can only be assessed if these habitats are monitored through time. This study establishes a baseline for monitoring the spawning activity of fish in the MPAs adjacent to Scripps Institution of Oceanography (La Jolla, CA, USA) by sampling fish eggs from the plankton. Using vertical plankton net tows, 266 collections were made from the Scripps Pier between 23 August 2012 and 28 August 2014; a total of 21,269 eggs were obtained. Eggs were identified using DNA barcoding: the COI or 16S rRNA gene was amplified from individual eggs and sequenced. All eggs that were successfully sequenced could be identified from a database of molecular barcodes of California fish species, resulting in species-level identification of 13,249 eggs. Additionally, a surface transport model of coastal circulation driven by current maps from high frequency radar was used to construct probability maps that estimate spawning locations that gave rise to the collected eggs. These maps indicated that currents usually come from the north but water parcels tend to be retained within the MPA; eggs sampled at the Scripps Pier have a high probability of having been spawned within the MPA. The surface transport model also suggests that although larvae have a high probability of being retained within the MPA, there is also significant spillover into nearby areas outside the MPA. This study provides an important baseline for addressing the extent to which spawning patterns of coastal California species may be affected by future changes in the ocean environment.

Previous seascape genetics studies have emphasized the role of ocean currents and geographic distances to explain the genetic structure of marine species, but the role of benthic habitat has been more rarely considered. Here, we compared the population genetic structure observed in West Pacific giant clam populations against model simulations that accounted habitat composition and configuration, geographical distance, and oceanic currents. Dispersal determined by geographical distance provided a modelled genetic structure in better agreement with the observations than dispersal by oceanic currents, possibly due to insufficient spatial resolution of available oceanographic and coastal circulation models. Considering both habitat composition and configuration significantly improved the match between simulated and observed genetic structures. This study emphasizes the importance of a reefscape genetics approach to population ecology, evolution and conservation in the sea.

The Finite Volume Community Ocean Model (FVCOM) was adapted to the Northern South China Sea (NSCS) to investigate the seasonality of coastal circulation, as well as along-shelf and cross-shelf transport. In fall and winter, southwestward current dominates the NSCS shelf, while the current’s direction shifts to northeast in summer. The circulation pattern in spring is more complicated: both southwestward and northeastward currents are detected on the NSCS shelf. The mean shelf circulation pattern in winter does not show the permanent counter-wind South China Sea Warm Current (SCSWC) along the 100–200 m isobaths. Meanwhile, the model results indicate a northeastward current flowing along 50–100 m isobaths in spring. Southwestward along-shelf transport varies from 0.30–1.93 Sv in fall and winter, and it redirects to northeast in summer ranging from 0.44–1.09 Sv. Onshore transport is mainly through the shelf break segment southeast of the Pearl River Estuary.

In this work, a multi-parameter inter-comparison of diverse ocean forecast models was conducted at the sea surface ranging from global to local scales in a two-phase stepwise strategy. Firstly, a comparison of CMEMS GLOBAL and the nested CMEMS IBI regional system was performed against satellite-derived and in situ observations. Results highlighted the overall benefits of both the GLOBAL direct data assimilation in open water and the increased horizontal resolution of IBI in coastal areas. Besides, IBI (Iberia–Biscay–Ireland) proved to capture shelf dynamics by better representing the horizontal extent and strength of a river freshwater plume, according to the results derived from the validation against in situ observations from a buoy moored in NW Spain. Secondly, a multi-model inter-comparison exercise for 2017 was performed in the Strait of Gibraltar among GLOBAL, IBI, and SAMPA (Sánchez-Garrido et al., 2013) high-resolution coastal forecast systems (partially nested to IBI) in order to elucidate the accuracy of each system to characterize the Atlantic Jet (AJ) inflow dynamics. A quantitative validation against hourly currents from high-frequency radar (HFR) highlighted both the steady improvement in AJ representation in terms of speed and direction when zooming from global to coastal scales through a multi-nesting model approach and also the relevance of a variety of factors at local scale such as a refined horizontal resolution, a tailored bathymetry, and a higher spatio-temporal resolution of the atmospheric forcing. The ability of each model to reproduce a 2 d quasi-permanent full reversal of the AJ surface inflow was examined in terms of wind-induced circulation patterns. SAMPA appeared to better reproduce the reversal events detected with HFR estimations, demonstrating the added value of imposing accurate meteorologically driven barotropic velocities in the open boundaries (imported from the NIVMAR (Álvarez-Fanjul et al., 2001) storm surge model) to take into account the remote effect of the atmospheric forcing over the entire Mediterranean basin, which was only partially included in IBI and GLOBAL systems. Finally, SAMPA coastal model outputs were also qualitatively analysed in the western Alboran Sea to put in a broader perspective the context of the onset, development, and end of such flow reversal episodes.

Interaction of tidal flow with a complex topography and bathymetry including headlands, islands, coral reefs and shoals create a rich submesoscale field of tidal jets, vortices, unsteady wakes, lee eddies and free shear layers, all of which impact marine ecology. A unique and detailed view of the submesoscale variability in a part of the Great Barrier Reef lagoon, Australia, that includes a number of small islands was obtained by using a “stereo” pair of 2-m-resolution visible-band images that were acquired just 54 s apart by the WorldView-3 satellite. Near-surface current and vorticity were extracted at a 50-m-resolution from those data using a cross-correlation technique and an optical-flow method, each yielding a similar result. The satellite-derived data are used to test the ability of the second-generation Louvain-la-Neuve ice-ocean model (SLIM), an unstructured-mesh, finite element model for geophysical and environmental flows, to reproduce the details of the currents in the region. The model succeeds in simulating the large-scale (> 1 km) current patterns, such as the main current and the width and magnitude of the jets developing in the gaps between the islands. Moreover, the order of magnitude of the vorticity and the occurrence of some vortices downstream of the islands are correctly reproduced. The smaller scales (< 500 m) are resolved by the model, although various discrepancies with the data are observed. The smallest scales (< 50 m) are unresolved by both the model- and image-derived velocity fields. This study shows that high-resolution models are able to a significant degree to simulate accurately the currents close to a rugged coast. Very-high-resolution satellite oceanography stereo images offer a new way to obtain snapshots of currents near a complex topography that has reefs, islands and shoals, and is a potential resource that could be more widely used to assess the predictive ability of coastal circulation models.

A combination of a three-dimensional Eulerian ocean circulation model (Princeton ocean model, POM) and a Lagrangian particle-tracking model (Surface-Trapped River Plume Evolution, STRiPE) is used to study the fate of fine river sediments discharged by the Peinan River at the southeastern coast of the island of Taiwan. The composite model is verified against in situ measurements and applied to simulate primary sediment deposition under freshet and typhoon discharge conditions of the Peinan River. It is shown that local wind plays a crucial role in sediment transport and settling in the coastal area through its influence on the river plume dynamics and turbulent mixing in the upper layer. Wind forcing conditions generally determine the location of the sediment deposit area, while its final pattern is defined by coastal circulation as modulated by the geometry of the coast and local bathymetry. In the study, region river-borne sediments are deposited to the sea floor, mainly in the shallow shelf areas. A significant portion of discharged fine sediments is moved offshore to the deeper ocean where it is further advected and dispersed by strong coastal circulation, mainly governed by the Kuroshio Current.The performed numerical experiments showed that sediment accumulation rate under typhoon conditions is about 2 orders of magnitude greater compared to freshet conditions. Based on the simulation results, we identified areas of continental shelf and continental slope adjacent to the Peinan River estuary which exhibit a high risk of formation of submarine landslides during and shortly after the typhoon events.

In this paper we present the Oceanographic Multipurpose Software Environment (OMUSE). OMUSE aims to provide a homogeneous environment for existing or newly developed numerical ocean simulation codes, simplifying their use and deployment. In this way, numerical experiments that combine ocean models representing different physics or spanning different ranges of physical scales can be easily designed. Rapid development of simulation models is made possible through the creation of simple high-level scripts. The low-level core of the abstraction in OMUSE is designed to deploy these simulations efficiently on heterogeneous high-performance computing resources. Cross-verification of simulation models with different codes and numerical methods is facilitated by the unified interface that OMUSE provides. Reproducibility in numerical experiments is fostered by allowing complex numerical experiments to be expressed in portable scripts that conform to a common OMUSE interface. Here, we present the design of OMUSE as well as the modules and model components currently included, which range from a simple conceptual quasi-geostrophic solver to the global circulation model POP (Parallel Ocean Program). The uniform access to the codes' simulation state and the extensive automation of data transfer and conversion operations aids the implementation of model couplings. We discuss the types of couplings that can be implemented using OMUSE. We also present example applications that demonstrate the straightforward model initialization and the concurrent use of data analysis tools on a running model. We give examples of multiscale and multiphysics simulations by embedding a regional ocean model into a global ocean model and by coupling a surface wave propagation model with a coastal circulation model.

Wanquan River is a small river located in Hainan, a tropical island in China. As the third largest river in Hainan, the river plume plays an important role in the regional terrigenous mass transport, coastal circulation, and the coral reef's ecosystem. Studies have shown that wind forcings significantly influence river plume dynamics. In this study, wind effects on the dispersal of the river plume and freshwater transport were examined numerically using a calibrated, unstructured, finite volume numerical model (FVCOM). Both wind direction and magnitude were determined to influence plume dispersal. Northeasterly (downwelling-favorable) winds drove freshwater down-shelf while southeasterly (onshore) winds drove water up-shelf (in the sense of Kelvin wave propagation) , and were confined near the coast. Southwesterly (upwelling-favorable) and northwesterly (offshore) winds transport more freshwater offshore. The transport flux is decomposed into an advection, a vertical shear, and an oscillatory component. The advection flux dominates the freshwater transport in the coastal area and the vertical shear flux is dominant in the offshore area. For the upwelling-favorable wind, the freshwater transport becomes more controlled by the advection transport with an increase in wind stress, due to enhanced vertical mixing. The relative importance of wind forcing and buoyancy force was investigated. It was found that, when the Wedderburn number is larger than one, the plume was dominated by wind forcing, although the importance of wind varies in different parts of the plume. The water column stratification decreased as a whole under the prevailing southwesterly wind, with the exception of the up-shelf and offshore areas.