Meso-scale testing and development of test procedures to maintain mass balance

The Conrad Blucher Institute for Surveying and Science (Texas A&M University––Corpus Christi) has conducted numerous petroleum experiments at the Shoreline Environmental Research Facility (Corpus Christi, Texas, USA). The meso-scale facility has multiple wave tanks, permitting some control in experimental design of the investigations, but allowing for real-world conditions. This paper outlines the evolution of a materials balance approach in conducting petroleum experiments at the facility. The first attempt at a materials balance was during a 1998 study on the fate/effects of dispersant use on crude oil. Both water column and beach sediment samples were collected. For the materials balance, the defined environmental compartments for oil accumulation were sediments, water column, and the water surface, while the discharge from the tanks was presumed to be the primary sink. The “lessons learned” included a need to quantify oil adhesion to the tank surfaces. This was resolved by adhering strips of the polymer tank lining to the tank sides that could be later removed and extracted for oil. Also, a protocol was needed to quantify any floating oil on the water surface. A water surface (oil slick) quantification protocol was developed, involving the use of solid-phase extraction disks. This protocol was first tested during a shoreline cleaner experiment, and later refined in subsequent dispersant effectiveness studies. The effectiveness tests were designed to simulate shallow embayments which created the need for additional adjustments in the tanks. Since dispersant efficacy is largely affected by hydrodynamics, it was necessary to scale the hydrodynamic conditions of the tanks to those expected in our prototype system (Corpus Christi Bay, Texas). The use of a scaled model permits the experiment to be reproduced and/or evaluated under different conditions. To minimize wave reflection in the tank, a parabolic wave dissipater was built. In terms of materials balance, this design reduced available surface area as a sink for oil adsorption.     

Mixing,hypersalinity and gradients in Hervey Bay,Australia

Hervey Bay, a large coastal embayment situated off the central eastern coast of Australia, is a shallow tidal area (average depth = 15 m), close to the continental shelf. It shows features of an inverse estuary, due to the high evaporation rate (approx. 2 m/year), low precipitation (less than 1 m/year) and on average almost no freshwater input from rivers that drain into the bay. The hydro- and thermodynamical structures of Hervey Bay and their variability are presented here for the first time, using a combination of four-dimensional modelling and observations from field studies. The numerical studies are performed with the Coupled Hydrodynamical Ecological Model for Regional Shelf Seas (COHERENS). Due to the high tidal range (>3.5 m), the bay is considered as a vertically well-mixed system, and therefore, only horizontal fronts are likely. Recent field measurements, but also the numerical simulations, indicate characteristic features of an inverse/hypersaline estuary with low salinity (35.5 psu) in the open ocean and peak values (>39.0 psu) in the head water of the bay. The model further predicts a nearly persistent mean salinity gradient of 0.5 psu across the bay (with higher salinities close to the shore). The investigation further shows that air temperature, wind direction and tidal regime are mainly responsible for the stability of the inverse circulation and the strength of the salinity gradient across the bay. Due to an ongoing drying trend, the occurrence of severe droughts at the central east coast of Australia and, therefore, a reduction in freshwater supply, the salinity flux out of the bay has increased, and the inverse circulation has also strengthened.     

A three-dimensional discontinuous Galerkin model applied to the baroclinic simulation of Corpus Christi Bay

In this work, we present results of a numerical study of Corpus Christi Bay, Texas and surrounding regions and compare simulated model results to recorded data. The validation data for the year 2000 include the water elevation, velocity, and salinity at selected locations. The baroclinic computations were performed using the University of Texas Bays and Estuaries 3D (UTBEST3D) simulator based on a discontinuous Galerkin finite element method for unstructured prismatic meshes. We also detail some recent advances in the modeling capabilities of UTBEST3D, such as a novel turbulence scheme and the support for local vertical discretization on parts of the computational domain. All runs were conducted on parallel clusters; an evaluation of parallel performance of UTBEST3D is included.     

Modelling residence‐time response to freshwater input in Apalachicola Bay,Florida, USA

Residence time of an estuary can be used to estimate the rate of removal of freshwater and pollutants from river inflow. In this study, a calibrated three‐dimensional hydrodynamic model was used to determine residence time in response to the change of freshwater input in Apalachicola Bay. The bay is about 40 km long and 7 km wide, with an average 3 m water depth. Through hydrodynamic model simulations, the spatial and temporal salinity and the total freshwater volume in the bay were calculated. Then the freshwater fraction method was used to estimate the residence time. Results indicate that the residence time in Apalachicola Bay typically ranges between 3 and 10 days for the daily freshwater input ranging from 177 m³/s to 4561 m³/s. Regression analysis of model results shows that an exponential regression equation can be used to correlate the estuarine residence time to changes of freshwater input. Copyright © 2002 John Wiley & Sons, Ltd.     

Trace metals in sediments of Raritan bay

Marine sediments are the ultimate recipient of nearly all trace metals introduced by man into aquatic ecosystems. This study examined the amounts and distribution of six trace metals (Cd, Cr, Cu, Ni, Pb, Zn) in sediments of Raritan Bay, apolluted estuary. The highest levels of these metals found in Raritan Bay were: Cd-15, Cr-260, Cu-1230, Ni-50, Pb-985, Zn-815. Three metals regimes within Raritan Bay are readily apparent. An area of high values extends across the Bay from the mouth of the Raritan Riverand Arthur Killinto Sandy Hook Bay. This is bounded on the south and northeast by areas of somewhat lower concentrations. An area of relatively low concentrations, near background values, occupies the region at the mouth of the Bay between Sandy Hook peninsula and Coney Island, New York. Metals values from Raritan Bay are compared with other areas and with a few exceptions, the Raritan Bay maximum levels were similar in magnitude to those of areas in Corpus Christi Harbour (U.S.A), Severn Estuary (U.K.), Deep Sea and Florida Lakes, River Blyth (U.K.), dump sites off New York City, various basins off South California, and in Long Island Sound.     

Distribution,characteristics and potential impacts of chromophoric dissolved organic matter (CDOM) in Hudson Strait and Hudson Bay,Canada

The characteristics of chromophoric dissolved organic matter (CDOM) were studied in Hudson Bay and Hudson Strait in the Canadian Arctic. Hudson Bay receives a disproportionately large influx of river runoff. With high dissolved organic matter (DOM) concentrations in Arctic rivers the influence of CDOM on coastal and ocean systems can be significant, yet the distribution, characteristics and potential consequences of CDOM in these waters remain unknown. We collected 470 discrete water samples in offshore, coastal, estuarine and river waters in the region during September and October 2005. Mixing of CDOM appeared conservative with salinity, although regional differences exist due to variable DOM composition in the rivers discharging to the Bay and the presence of sea-ice melt, which has low CDOM concentrations and low salinity. There were higher concentrations of CDOM in Hudson Bay, especially in coastal waters with salinities <28$<28$, due to river runoff. Using CDOM composition of water masses as a tracer for the freshwater components revealed that river runoff is largely constrained to nearshore waters in Hudson Bay, while sea-ice melt is distributed more evenly in the Bay. Strong inshore–offshore gradients in the bio-optical properties of the surface waters in the Hudson Bay cause large variation in penetration of ultraviolet radiation and the photic depth within the bay, potentially controlling the vertical distribution of biomass and occurrence of deep chlorophyll maxima which are prevalent only in the more transparent offshore waters of the bay. The CDOM distribution and associated photoprocesses may influence the thermodynamics and stratification of the coastal waters, through trapping of radiant heating within the top few meters of the water column. Photoproduction of biologically labile substrates from CDOM could potentially stimulate the growth of biomass in Hudson Bay coastal waters. Further studies are needed to investigate the importance of terrestrial DOM in the Hudson Bay region, and the impact of hydroelectric development and climate change on these processes.     

Progressive change of tidal wave characteristics from the eastern Yellow Sea to the Asan Bay,a strongly convergent bay in the west coast of Korea

Although there have been studies on the tide in convergent bay (or estuary), the tide change in terms of phase speed, amplitude, and phase difference between elevation and tidal current from a coastal ocean to a convergent bay has not been clearly shown so far. This study systematically examines the change of tidal wave characteristics from the eastern Yellow Sea to the Asan Bay, a strongly convergent bay on the west coast of Korea, using observations and an analytical model. As the tidal wave propagates from the eastern Yellow Sea into the Asan Bay, the phase speed, amplitude, and phase difference between elevation and tidal current increase along the channel. Such a phenomenon represents a unique example of tide change from a coastal ocean to a convergent bay, indicating dominance of convergence over friction in the Asan Bay. Both analytically computed tidal amplitude and travelling time compare well with observations. In the Asan Bay, the influence of the reflected wave is only felt in the upper one fifth of the bay and is almost unperceivable in the rest of the bay. The analytical analyses presented in this paper are particularly useful for understanding the relative importance of channel convergence, bottom friction, and reflected wave on the tidal characteristics change along the channel and the proposed method could be applicable to other estuaries.     

Scales and structure of frontal adjustment and freshwater export in a region of freshwater influence

Sea surface temperature satellite imagery and a regional hydrodynamic model are used to investigate the variability and structure of the Liverpool Bay thermohaline front. A statistically based water mass classification technique is used to locate the front in both data sets. The front moves between 5 and 35 km in response to spring–neap changes in tidal mixing, an adjustment that is much greater than at other shelf-sea fronts. Superimposed on top of this fortnightly cycle are semi-diurnal movements of 5–10 km driven by flood and ebb tidal currents. Seasonal variability in the freshwater discharge and the density difference between buoyant inflow and more saline Irish Sea water give rise to two different dynamical regimes. During winter, when cold inflow reduces the buoyancy of the plume, a bottom-advected front develops. Over the summer, when warm river water provides additional buoyancy, a surface-advected plume detaches from the bottom and propagates much larger distances across the bay. Decoupled from near-bed processes, the position of the surface front is more variable. Fortnightly stratification and re-mixing over large areas of Liverpool Bay is a potentially important mechanism by which freshwater, and its nutrient and pollutant loads, are exported from the coastal plume system. Based on length scales estimated from model and satellite data, the erosion of post-neap stratification is estimated to be responsible for exporting approximately 19% of the fresh estuarine discharge annually entering the system. Although the baroclinic residual circulation makes a more significant contribution to freshwater fluxes, the episodic nature of the spring–neap cycle may have important implications for biogeochemical cycles within the bay.     

Simulation of eutrophication and associated occurrence of hypoxic and anoxic condition in a coastal bay in Japan

A probabilistic method of calculating the occurrence of oxygen-depleted water within a combined hydrothermal and water quality model was presented in this paper to investigate the environmental impact of eutrophication on the living resources. The method was applied to an eutrophicated shallow coastal bay in western Japan, where the occurrence of red tides at the water surface and the onset of bottom hypoxic waters are observed every summer. Both meteorology and freshwater inflow contribute to the development of stratification of the bay, thus limiting the dissolved oxygen supply to bottom waters. The resulting hydrodynamics enhances the development of oxygen-depleted bottom waters by transporting organic matter produced by algal blooms to the inner bay, where it decomposes and exerts high SOD. During August, about 60% of the inner bay is hypoxic for prolonged durations and as a result most of the benthic biota and fish die. The method used here is a very useful and informative way to evaluate the spatial and temporal damage and severity caused by hypoxia on living resources. Moreover, the model results agreed very well with the observed hydrodynamics, thermal structure and water quality data of the stratified bay. The model can be used for other lakes and bays where knowledge of temperature and density stratification is important for assessing water quality.     

Some challenges of an "upside down" nitrogen budget--science and management in Greenwich Bay, RI (USA)

When nutrients impact estuarine water quality, scientists and managers instinctively focus on quantifying and controlling land-based sources. However, in Greenwich Bay, RI, the estuary opens onto a larger and more intensively fertilized coastal water body (Narragansett Bay). Previous inventories of nitrogen (N) inputs to Greenwich Bay found that N inputs from Narragansett Bay exceeded those from the local watershed, suggesting that recent efforts to reduce local watershed N loads may have little effect on estuarine water quality. We used stable isotopes of N to characterize watershed and Narragansett Bay N sources as well as the composition of primary producers and consumers throughout Greenwich Bay. Results were consistent with previous assessments of the importance of N inputs to Greenwich Bay from Narragansett Bay. As multiple N sources contribute to estuarine water quality, effective management requires attention to individual sources commensurate with overall magnitude, regardless of the political complications that may entail.     

Size-fractionated phytoplankton biomass,primary production and respiration in the Nervión–Ibaizabal estuary: A comparison with other nearshore coastal and estuarine ecosystems from the Bay of Biscay

The seasonal pattern of size-fractionated phytoplankton biomass, primary production and respiration was investigated along the longitudinal axis of the Nervión–Ibaizabal estuary (Bay of Biscay) from April 2003 to September 2004. Environmental factors influencing phytoplankton dynamics were also studied. Chlorophyll a biomass showed a longitudinal pattern of increase from the outer Abra bay to the inner estuary. On a seasonal scale, in the intermediate and inner estuary phytoplankton biomass maxima were registered in summer, the warmest and driest season, whereas in the outer bay chlorophyll a peaks occurred in May 2004, but were delayed to August 2003, likely due to a very rainy spring. Data suggest that river flow exerts a marked influence on the timing of phytoplankton biomass maxima in this estuary, decreased river flows providing a lowering of turbidity and an increase in water residence time needed for chlorophyll a to build up. Nutrient concentrations were high enough not to limit phytoplankton growth throughout the annual cycle, except silicate and occasionally phosphate in the outer bay during summer. Silicate concentration correlated positively with river flow, whereas ammonium and phosphate maximum values were generally measured in the mid-estuary, suggesting the importance of allochthonous anthropogenic sources. In the intermediate and inner estuary phytoplankton biomass was generally dominated by >8 μm size-fraction (ca. 60%), but in August 2003 <8 μm size-fraction increased its contribution in the intermediate estuary. It is argued that the lower nutrient concentrations measured in August 2003 than in August 2004 could have played a role. This is the first study in which phytoplankton primary production rates have been measured along the longitudinal axis of the Nervión–Ibaizabal estuary. Throughout the annual cycle these rates ranged from 0.001 to 3.163 g C m^?3 d^?1 and were comparable to those measured in nearby small estuaries of the Basque coast and other larger estuaries on the Bay of Biscay. Surface plankton community respiration rate maxima were measured during the spring 2004 chlorophyll a peak in the Abra bay and in summer months at the mid and inner estuary, coinciding with chlorophyll a biomass and primary production maxima. In general, respiration rates showed a positive correlation with temperature. In order to compare results from the Nervión–Ibaizabal estuary with other nearshore coastal and estuarine ecosystems within the Bay of Biscay a review of existing information on phytoplankton biomass and primary production dynamics was performed.     

Groundwater travel time in the freshwater lenses of Samborombón Bay,Argentina

Abstract

The Samborombón Bay area (Argentina) is a coastal plain environment that contains groundwater resources with high salinity. In addition, there are local freshwater lenses associated with shell ridges and sand sheets in the region. In this work, the groundwater travel time in these freshwater lenses is estimated based on their geological conditions, which include hydraulic conductivity, recharge, morphology and discharge to surface freshwater or to saline groundwater. Groundwater travel times in the freshwater lenses were calculated from the equations developed by Chesnaux and Allen. The travel times estimated for the different scenarios were relatively short. The results indicate that the groundwater flow tends to be strongly dependent on the recharge conditions, with an excess of water in the water balance. The results can be applied to help design sustainable management methods to exploit this water resource system and also to assess the impact of contaminant plumes on this groundwater resource.

Citation Carol, E., Kruse, E. & Roig, A. (2010) Groundwater travel time in the freshwater lenses of Samborombón Bay, Argentina. Hydrol. Sci. J. 55(5), 754–762.     

Designing open water disposal for dredged muddy sediments

Open water disposal of muddy sediments in the estuarine environment is practiced to minimize dredging costs and to preserve contained disposal site capacity. Open water sites are usually either dispersive or retentive. Dispersive sites are used in the expectation that disposed sediments will not remain there, but will be transported out of the site, leaving room for additional disposal. Retentive sites are designed to ensure that disposed sediments mostly remain within the site. Choice of one of these approaches depends on the site character, sediment character, and disposal quantities. Design of disposal management plans for both site types is accomplished by use of field observations, laboratory tests, and numerical modeling.Three disposal site studies illustrate the methods used. At the Alcatraz site in San Francisco Bay, a dispersive condition is maintained by use of constraints on dredged mud characteristics that were developed from laboratory tests on erosion rates and from numerical modeling of the dump process. Field experiments were designed to evaluate the management procedure. In Corpus Christi Bay a numerical model was used to determine how much disposed sediment returns to the navigation channel, and to devise a location for disposal that will minimize that return. In Puget Sound a model has been used to ensure that most of the disposed material remains in the site. New techniques, including a piped disposal through 60 m of water, were investigated.     

Bottom currents at the entrance to False Bay, South Africa

False Bay, the biggest bay in South Africa, has to accommodate various demands in terms of recreation, naval activities and fisheries while it is lately also exposed to increased pollution. To determine the currents at the entrance to the Bay and thus obtain insight into the dynamics of the region, the flushing rate of the Bay and other aspects of the circulation, a number of current meters were deployed in the lower half of the water column at the entrance during the austral summer of 1986/1987. The results of these measurements, augmented and supported by temperature-salinity sections and meteorologic measurements in the vicinity, are discussed and compared with historical observations of the currents and water properties in the Bay.     

Simulation of submarine ground water discharge to a marine estuary: Biscayne Bay, Florida

Variable density ground water flow models are rarely used to estimate submarine ground water discharge because of limitations in computer speed, data availability, and availability of a simulation tool that can minimize numerical dispersion. This paper presents an application of the SEAWAT code, which is a combined version of MODFLOW and MT3D, to estimate rates of submarine ground water discharge to a coastal marine estuary. Discharge rates were estimated for Biscayne Bay, Florida, for the period from January 1989 to September 1998 using a three-dimensional, variable density ground water flow and transport model. Hydrologic stresses in the 10-layer model include recharge, evapotranspiration, ground water withdrawals from municipal wellfields, interactions with surface water (canals in urban areas and wetlands in the Everglades), boundary fluxes, and submarine ground water discharge to Biscayne Bay. The model was calibrated by matching ground water levels in monitoring wells, baseflow to canals, and the position of the 1995 salt water intrusion line. Results suggest that fresh submarine ground water discharge to Biscayne Bay may have exceeded surface water discharge during the 1989, 1990, and 1991 dry seasons, but the average discharge for the entire simulation period was only approximately 10% of the surface water discharge to the bay. Results from the model also suggest that tidal canals intercept fresh ground water that might otherwise have discharged directly to Biscayne Bay. This application demonstrates that regional scale variable density models are potentially useful tools for estimating rates of submarine ground water discharge.     

Spatial and temporal variation in hexachlorocyclohexane isomers in a temperate estuary

Hexachlorocylcohexanes (HCHs) are pesticides that persist in air and water of the Northern hemisphere. To understand the spatial and temporal variability in HCH levels in estuarine surface waters we measured concentrations of two HCH isomers (-HCH and γ-HCH) at six sites in the York River estuary at bimonthly intervals for a year. Bacterial abundance and activity were also monitored using acridine orange direct counts and uptake of tritiated substrates, respectively. -HCH was consistently observed to be significantly higher in marine water compared to river water entering the estuary, suggesting that the Chesapeake Bay or Atlantic Ocean is a larger source of this compound to the York River estuary compared to riverine input. Moreover, following periods of high freshwater flow into the estuary during spring and early summer, both - and γ-HCH mixing curves indicated an additional source of these pollutants to the estuary such as land-derived runoff or groundwater discharge. In contrast, during low freshwater flow (late summer and fall) the estuary was a sink for HCHs, with γ-HCH more rapidly removed from the estuary than -HCH. During the period of low freshwater flow, concentrations of both - and γ-HCH were negatively correlated with bacterial activity. Bacterial activity as opposed to abundance appears to control HCH degradation in estuarine surface waters.     

A Challenge of Water Purification in Dokai Bay, Japan

A history of water pollution and countermeasures for water purification in Dokai Bay, Japan are reviewed. Now, Dokai Bay suffers from the occurrences of red tides and oxygen-deficiency in summer. In order to prevent the occurrences of red tides and oxygen-deficiency, an ecological numerical model has been developed. The model experiments forecast that when the phosphorus or nitrogen load from land will be cut by 90% or 95%, respectively, red tides and oxygen-deficiency will not occur in Dokai Bay. If the industrial and sewage facilities are not sufficient to cut the nutrients load to the necessary degree, we have to consider other countermeasures such as cultivating bivalves and algae in order to decrease the nutrients concentration in the bay. International co-operation related to coastal zone management is also discussed.     

Numerical modeling of tidal currents, sediment transport and morphological evolution in Hangzhou Bay, China

A 2D depth-averaged numerical model is set up to simulate the macro-scale hydrodynamic characteristics, sediment transport patterns and morphological evolution in Hangzhou Bay, a large macro-tidal estuary on the eastern coast of China. By incorporating the shallow water equations, the suspended sediment transport equation and the mass-balance equation for sediment; short-term hydrodynamics, sediment transport and long-term morphological evolution for Hangzhou Bay are simulated and the underlying physical mechanisms are analyzed. The model reproduces the spatial distribution patterns of suspended sediment concentration (SSC) in Hangzhou Bay, characterized by three high SSC zones and two low SSC zones. It also correctly simulates the residual flow, the residual sediment transport and the sediment accumulation patterns in Hangzhou Bay. The model results are in agreement with previous studies based on field measurements. The residual flow and the residual sediment transport are landwards directed in the northern part of the bay and seawards directed in the southern part. Sediment accumulation takes place in most areas of the bay. Harmonic analysis revealed that the tide is flood-dominant in the northern part of the bay and ebb-dominant in the southern part of the bay. The strength of the flood-dominance increases landwards along the northern Hangzhou Bay. In turn sediment transport in Hangzhou Bay is controlled by this tidal asymmetry pattern. In addition, the direction of tidal propagation in the East China Sea, the presence of the archipelago in the southeast and the funnel-shaped geometry of the bay, play important roles for the patterns of sediment transport and sediment accumulation respectively.     

Transport of oceanic nitrate from the continental shelf to the coastal basin in relation to the path of the Kuroshio

Hydrographic and biogeochemical observations were conducted along the longitudinal section from Ise Bay to the continental margin (southern coast of Japan) to investigate changes according to the Kuroshio path variations during the summer. The strength of the uplift of the cold deep water was influenced by the surface intrusion of the Kuroshio water to the shelf region. When the intrusion of the Kuroshio surface water to the shelf region was weak in 2006, the cold and NO₃⁻-rich shelf water intruded into the bottom layer in the bay from the shelf. This bottom intrusion was intensified by the large river discharge. The nitrogen isotope ratio (δ¹⁵N) of NO₃⁻ (4–5‰) in the bottom bay water was same as that in the deeper NO₃⁻ over the shelf, indicating the supply of new nitrogen to the bay. The warm and NO₃⁻-poor shelf water intruded into the middle layer via the mixing region at the bay mouth when the Kuroshio water distributed in the coastal areas off Ise Bay in 2005. The regenerated NO₃⁻ with isotopically light nitrogen (δ¹⁵N=−1‰) was supplied from the shelf to the bay. This NO₃⁻ is regenerated by the nitrification in the upper layer over the shelf. The contribution rate of regenerated NO₃⁻ over the shelf to the total NO₃⁻ in the subsurface chlorophyll maximum layer in the bay was estimated at 56% by a two-source mixing model coupled with the Rayleigh equation.     

The long-term salinity field in San Francisco Bay

Data are presented on long-term salinity behaviour in San Francisco Bay, California. A two-level, width averaged model of the tidally averaged salinity and circulation has been written in order to interpret the long-term (days to decades) salinity variability. The model has been used to simulate daily averaged salinity in the upper and lower levels of a 51 segment discretization of the Bay over the 22-yr period 1967–1988. Monthly averaged surface salinity from observations and monthly-averaged simulated salinity are in reasonable agreement. Good agreement is obtained from comparison with daily averaged salinity measured in the upper reaches of North Bay.The salinity variability is driven primarily by freshwater inflow with relatively minor oceanic influence. All stations exhibit a marked seasonal cycle in accordance with the Mediterranean climate, as well as a rich spectrum of variability due to extreme inflow events and extended periods of drought. Monthly averaged salinity intrusion positions have a pronounced seasonal variability and show an approximately linear response to the logarithm of monthly averaged Delta inflow. Although few observed data are available for studies of long-term salinity stratification, modelled stratification is found to be strongly dependent on freshwater inflow; the nature of that dependence varies throughout the Bay. Near the Golden Gate, stratification tends to increase up to very high inflows. In the central reaches of North Bay, modelled stratification maximizes as a function of inflow and further inflow reduces stratification. Near the head of North Bay, lowest summer inflows are associated with the greatest modelled stratification. Observations from the central reaches of North Bay show marked spring-neap variations in stratification and gravitational circulation, both being stronger at neap tides. This spring-neap variation is simulated by the model. A feature of the modelled stratification is a hysteresis in which, for a given spring-neap tidal range and fairly steady inflows, the stratification is higher progressing from neaps to springs than from springs to neaps.The simulated responses of the Bay to perturbations in coastal sea salinity and Delta inflow have been used to further delineate the time-scales of salinity variability. Simulations have been performed about low inflow, steady-state conditions for both salinity and Delta inflow perturbations. For salinity perturbations a small, sinusoidal salinity signal with a period of 1 yr has been applied at the coastal boundary as well as a pulse of salinity with a duration of one day. For Delta inflow perturbations a small, sinusoidally varying inflow signal with a period of 1 yr has been superimposed on an otherwise constant Delta inflow, as well as a pulse of inflow with a duration of one day. Perturbations in coastal salinity dissipate as they move through the Bay. Seasonal perturbations require about 40–45 days to propagate from the coastal ocean to the Delta and to the head of South Bay. The response times of the model to perturbations in freshwater inflow are faster than this in North Bay and comparable in South Bay. In North Bay, time-scales are consistent with advection due to lower level, up-estuary transport of coastal salinity perturbations; for inflow perturbations, faster response times arise from both upper level, down-estuary advection and much faster, down-estuary migration of isohalines in response to inflow volume continuity. In South Bay, the dominant time-scales are governed by tidal dispersion.