James A. Lerczak

Numerical modeling of an estuary : a comprehensive skill assessment

[i] Numerical simulations of the Hudson River estuary using a terrain-following, three-dimensional model (Regional Ocean Modeling System (ROMS)) are compared with an extensive set of time series and spatially resolved measurements over a 43 day period with large variations in tidal forcing and river discharge. The model is particularly effective at reproducing the observed temporal variations in both the salinity and current structure, including tidal, spring neap, and river discharge-induced variability. Large observed variations in stratification between neap and spring tides are captured qualitatively and quantitatively by the model. The observed structure and variations of the longitudinal salinity gradient are also well reproduced. The most notable discrepancy between the model and the data is in the vertical salinity structure. While the surface-to-bottom salinity difference is well reproduced, the stratification in the model tends to extend all the way to the water surface, whereas the observations indicate a distinct pycnocline and a surface mixed layer. Because the southern boundary condition is located near the mouth the estuary, the salinity within the domain is particularly sensitive to the specification of salinity at the boundary. A boundary condition for the horizontal salinity gradient, based on the local value of salinity, is developed to incorporate physical processes beyond the open boundary not resolved by the model. Model results are sensitive to the specification of the bottom roughness length and vertical stability functions, insofar as they influence the intensity of vertical mixing. The results only varied slightly between different turbulence closure methods of k-e, k-ω, and k-kl.

Modeling the lateral circulation in straight, stratified estuaries

Abstract The dynamics of lateral circulation in an idealized, straight estuary under varying stratification conditions is investigated using a three-dimensional, hydrostatic, primitive equation model in order to determine the importance of lateral circulation to the momentum budget within the estuary. For all model runs, lateral circulation is about 4 times as strong during flood tides as during ebbs. This flood–ebb asymmetry is due to a feedback between the lateral circulation and the along-channel tidal currents, as well as to time-varying stratification over a tidal cycle. As the stratification is increased, the lateral circulation is significantly reduced because of the adverse pressure gradient set up by isopycnals being tilted by the lateral flow itself. When rotation is included, a time-dependent, cross-channel Ekman circulation is driven, and the tidally averaged, bottom lateral circulation is enhanced toward the right bank (when looking toward the ocean in the Northern Hemisphere). This asymmetry...

Subtidal Salinity and Velocity in the Hudson River Estuary: Observations and Modeling

A tidally and cross-sectionally averaged model based on the temporal evolution of the quasi-steady Hansen and Rattray equations is applied to simulate the salinity distribution and vertical exchange flow along the Hudson River estuary. The model achieves high skill at hindcasting salinity and residual velocity variation during a 110-day period in 2004 covering a wide range of river discharges and tidal forcing. The approach is based on an existing model framework that has been modified to improve model skill relative to observations. The external forcing has been modified to capture meteorological time-scale variability in salinity, stratification, and residual velocity due to sea level fluctuations at the open boundary and alongestuary wind stress. To reflect changes in vertical mixing due to stratification, the vertical mixing coefficients have been modified to use the bottom boundary layer height rather than the water depth as an effective mixing length scale. The boundary layer parameterization depends on the tidal amplitude and the local baroclinic pressure gradient through the longitudinal Richardson number, and improves the model response to spring–neap variability in tidal amplitude during periods of high river discharge. Finally, steady-state model solutions are evaluated for both the Hudson River and northern San Francisco Bay over a range of forcing conditions. Agreement between the model and scaling of equilibrium salinity intrusions lends confidence that the approach is transferable to other estuaries, despite significant differences in bathymetry. Discrepancies between the model results and observations at high river discharge are indicative of limits at which the formulation begins to fail, and where an alternative approach that captures two-layer dynamics would be more appropriate.

Mechanisms driving the time-dependent salt flux in a partially stratified estuary

The subtidal salt balance and the mechanisms driving the downgradient salt flux in the Hudson River estuary are investigated using measurements from a cross-channel mooring array of current meters, temperature and conductivity sensors, and cross-channel and along-estuary shipboard surveys obtained during the spring of 2002. Steady (subtidal) vertical shear dispersion, resulting from the estuarine exchange flow, was the dominant mechanism driving the downgradient salt flux, and varied by over an order of magnitude over the spring–neap cycle, with maximum values during neap tides and minimum values during spring tides. Corresponding longitudinal dispersion rates were as big as 2500 m 2 s 1 during neap tides. The salinity intrusion was not in a steady balance during the study period. During spring tides, the oceanward advective salt flux resulting from the net outflow balanced the time rate of change of salt content landward of the study site, and salt was flushed out of the estuary. During neap tides, the landward steady shear dispersion salt flux exceeded the oceanward advective salt flux, and salt entered the estuary. Factor-of-4 variations in the salt content occurred at the spring–neap time scale and at the time scale of variations in the net outflow. On average, the salt flux resulting from tidal correlations between currents and salinity (tidal oscillatory salt flux) was an order of magnitude smaller than that resulting from steady shear dispersion. During neap tides, this flux was minimal (or slightly countergradient) and was due to correlations between tidal currents and vertical excursions of the halocline. During spring tides, the tidal oscillatory salt flux was driven primarily by oscillatory shear dispersion, with an associated longitudinal dispersion rate of about 130 m 2 s 1 .

The influence of lateral advection on the residual estuarine circulation : a numerical modeling study of the Hudson River Estuary

Abstract In most estuarine systems it is assumed that the dominant along-channel momentum balance is between the integrated pressure gradient and bed stress. Scaling the amplitude of the estuarine circulation based on this balance has been shown to have predictive skill. However, a number of authors recently highlighted important nonlinear processes that contribute to the subtidal dynamics at leading order. In this study, a previously validated numerical model of the Hudson River estuary is used to examine the forces driving the residual estuarine circulation and to test the predictive skill of two linear scaling relationships. Results demonstrate that the nonlinear advective acceleration terms contribute to the subtidal along-channel momentum balance at leading order. The contribution of these nonlinear terms is driven largely by secondary lateral flows. Under a range of forcing conditions in the model runs, the advective acceleration terms nearly always act in concert with the baroclinic pressure gradie...

Structure, variability, and salt flux in a strongly forced salt wedge estuary

This researchwas funded by National Science Foundation grant OCE‐0452054. Ralston also received partial support from The Penzance Endowed Fund in Support of Assistant Scientists and The John F. and Dorothy H. Magee Fund in Support of Scientific Staff at Woods Hole Oceanographic Institution.

Estuarine Boundary Layer Mixing Processes: Insights from Dye Experiments*

A series of dye releases in the Hudson River estuary elucidated diapycnal mixing rates and temporal variability over tidal and fortnightly time scales. Dye was injected in the bottom boundary layer for each of four releases during different phases of the tide and of the spring–neap cycle. Diapycnal mixing occurs primarily through entrainment that is driven by shear production in the bottom boundary layer. On flood the dye extended vertically through the bottom mixed layer, and its concentration decreased abruptly near the base of the pycnocline, usually at a height corresponding to a velocity maximum. Boundary layer growth is consistent with a one-dimensional, stress-driven entrainment model. A model was developed for the vertical structure of the vertical eddy viscosity in the flood tide boundary layer that is proportional to u 2 /N, where u * and N are the bottom friction velocity and buoyancy frequency above the boundary layer. The model also predicts that the buoyancy flux averaged over the bottom boundary layer is equal to 0.06N u 2 or, based on the structure of the boundary layer equal to 0.1NBLu 2 , where NBL is the buoyancy frequency across the flood-tide boundary layer. Estimates of shear production and buoyancy flux indicate that the flux Richardson number in the flood-tide boundary layer is 0.1–0.18, consistent with the model indicating that the flux Richardson number is between 0.1 and 0.14. During ebb, the boundary layer was more stratified, and its vertical extent was not as sharply delineated as in the flood. During neap tide the rate of mixing during ebb was significantly weaker than on flood, owing to reduced bottom stress and stabilization by stratification. As tidal amplitude increased ebb mixing increased and more closely resembled the boundary layer entrainment process observed during the flood. Tidal straining modestly increased the entrainment rate during the flood, and it restratified the boundary layer and inhibited mixing during the ebb.

The Temporal Response of the Length of a Partially Stratified Estuary to Changes in River Flow and Tidal Amplitude

The temporal response of the length of a partially-mixed estuary to changes in freshwater discharge, Qf , and tidal amplitude, UT , is studied using a 108 day time series collected along the length of the Hudson River estuary in the spring and summer of 2004 and a long-term (13.4 year) record of Qf , UT , and near-surface salinity. When Qf was moderately high, the tidally-averaged length of the estuary, L5, here defined as the distance from the mouth to the up-estuary location where the vertically-averaged salinity is five psu, fluctuated by more than 47 km over the spring-neap cycle, ranging from 28 km to >75 km. During low flow periods, L5 varied very little over the spring-neap cycle and approached a steady length. The response is quantified and compared to predictions of a linearized model derived from the global estuarine salt balance. The model is forced by fluctuations in Qf and UT relative to average discharge, Qo, and tidal amplitude, UTo, and predicts the linear response time scale, τ, and the steady-state length, Lo, for average forcing. Two vertical mixing schemes are considered, in which a) mixing is proportional to UT and b) dependence of mixing on stratification is also parameterized. Based on least-squares fits between L5 and estuary length predicted by the model, estimated τ varied by an order of magnitude from a period of high average discharge (Qo = 750 m3s-1, τ = 4.2 days) to a period of low discharge (Qo = 170 m3s-1, τ = 40.4 days). Over the range of observed discharge, Lo ∝ Qo-0.30±0.03, consistent with the theoretical scaling for an estuary whose landward salt flux is driven by vertical estuarine exchange circulation. Estimated τ was proportional to the discharge advection time scale (LoA/Qo, where A is the cross-sectional area of the estuary). However, τ was three to four times larger than the theoretical prediction. The model with stratification dependent mixing predicted variations in L5 with higher skill than the model with mixing proportional to UT . This model provides insight into the time dependent response of a partially-stratified estuary to changes in forcing and explains the strong dependence of the amplitude of the spring-neap response on freshwater discharge. However, the utility of the linear model is limited because it assumes a uniform channel and because the underlying dynamics are nonlinear and the forcing, Qf and UT , can undergo large amplitude variations. River discharge, in particular, can vary by over an order of magnitude over timescales comparable to or shorter than the response timescale of the estuary.

Environmental controls, oceanography and population dynamics of pathogens and harmful algal blooms: connecting sources to human exposure

Coupled physical-biological models are capable of linking the complex interactions between environmental factors and physical hydrodynamics to simulate the growth, toxicity and transport of infectious pathogens and harmful algal blooms (HABs). Such simulations can be used to assess and predict the impact of pathogens and HABs on human health. Given the widespread and increasing reliance of coastal communities on aquatic systems for drinking water, seafood and recreation, such predictions are critical for making informed resource management decisions. Here we identify three challenges to making this connection between pathogens/HABs and human health: predicting concentrations and toxicity; identifying the spatial and temporal scales of population and ecosystem interactions; and applying the understanding of population dynamics of pathogens/HABs to management strategies. We elaborate on the need to meet each of these challenges, describe how modeling approaches can be used and discuss strategies for moving forward in addressing these challenges.

Estuarine Exchange Flow Quantified with Isohaline Coordinates: Contrasting Long and Short Estuaries

AbstractIsohaline coordinate analysis is used to compare the exchange flow in two contrasting estuaries, the long (with respect to tidal excursion) Hudson River and the short Merrimack River, using validated numerical models. The isohaline analysis averages fluxes in salinity space rather than in physical space, yielding the isohaline exchange flow that incorporates both subtidal and tidal fluxes and precisely satisfies the Knudsen relation. The isohaline analysis can be consistently applied to both subtidally and tidally dominated estuaries. In the Hudson, the isohaline exchange flow is similar to results from the Eulerian analysis, and the conventional estuarine theory can be used to quantify the salt transport based on scaling with the baroclinic pressure gradient. In the Merrimack, the isohaline exchange flow is much larger than the Eulerian quantity, indicating the dominance of tidal salt flux. The exchange flow does not scale with the baroclinic pressure gradient but rather with tidal volume flux. T...