Model Development — SqueezeBox: A Simple Tool to Understand the Impacts of River Flow on Estuarine Salinity

Joan Sheldon and Merryl Alber (Dept of Marine Sciences, Univ of Georgia)

Project Overview: SqueezeBox is a desktop modeling tool developed by Merryl Alber and Joan Sheldon at the University of Georgia that can be used to evaluate the effects of freshwater inflow on the salinity distribution and mixing time scales of riverine estuaries.  Salinity is a master variable that affects many estuarine characteristics and is important to estuarine organisms.  Mixing time scales, such as residence time and flushing time, provide information on water movement that can be compared with the rates of processes that may act upon materials (such as nutrients or pollutants) as they are carried through the estuary.

SqueezeBox is useful for evaluating water quality questions because it can be used to determine how long it will take to reduce an initial pulse of a dissolved substance, such as a water-borne pollutant, to a percentage of its original concentration or to a specified standard.  The model can also be used to predict the expected distribution of the substance after a given amount of time.

Accomplishments: SqueezeBox generates 1-dimensional, tidally averaged box models with structures scalable for different river flows.  It is designed to be flexible and easily adaptable to different estuaries with minimal data requirements. The application is a compiled Microsoft Visual Basic program that runs under Microsoft Windows versions 95-XP (not tested on Vista), but the end user does not need Visual Basic. Estuary module development requires bathymetry, freshwater input rates, and salinity observations throughout the estuary at a range of freshwater flows. These data are used to develop descriptive equations of the along-channel variation in cross-sectional area and the response of the net up-estuary flow of seawater to freshwater inflow changes. These equations constitute an estuary module, which is supplied as text files read by application. Simple mixing equations are used to predict the salinity distribution for a chosen river flow, and the application generates a conventional box model with suitable box sizes and time step for stable numerical simulations. The user then specifies an initial distribution and optional sources of a simulated tracer, which could represent many dissolved substances. The tracer can be inert, or a first-order reaction rate can be specified for each box. Preset tracer distributions can be used to calculate several mixing time scales such as average residence time and turnover time.

SqueezeBox and modules for the Altamaha River estuary (GA) and the Ogeechee River estuary (GA) have been developed with funds from The Nature Conservancy, the Georgia Coastal Ecosystems LTER program (NSF), and the Georgia Dept. of Natural Resources Coastal Incentive Grant program (NOAA).

SqueezeBox is constantly being upgraded as new features are desired for ongoing research, and it is not yet packaged for wide distribution with integrated help functions, but the initial application and module development have been described in the following publications:

Simulating Material Movement through the Lower Altamaha River Estuary using a 1-D Box Model

1-D optimum-boundary box models were used to simulate the movement of dissolved pollutants or other conservatively mixing constituents through the Altamaha River estuary. Tracers were introduced into the models as point sources at various locations within the estuary and as a non-point input to the entire system. In each case, models were run at four different river flow rates and were used to simulate both the movement of tracer within the estuary and its rate of removal. When tracer was introduced at head of tide, it moved rapidly (from 1-2 d, depending on flow) to the head of the mixing zone 30 km downstream. Tracer released anywhere in the estuary, including farther downstream at 2 km, moved toward an area 4-6 km upstream of the mouth, where it remained centered as overall removal continued. Movement toward this zone was observed regardless of flow rate. Introduction of tracer as a non-point source also resulted in distributions centered at 4-6 km, suggesting that this area is a potential convergence zone in the Altamaha River estuary. Maximum exposure to tracer, measured as the amount of time that concentration exceeds a given threshold, depends on where in the estuary tracer is released. When released at head of tide, maximum exposure is experienced at 6-10 km. Simulations of the type presented here are useful for evaluating the conservative movements of both point- and non-point-source constituents in the estuary.

Sheldon, J. E. and M. Alber. 2003. Simulating Material Movement through the Lower Altamaha River Estuary using a 1-D Box Model. In K. J. Hatcher (ed.) Proceedings of the 2003 Georgia Water Resources Conference. Institute of Ecology, University of Georgia, Athens, Georgia.

A comparison of residence time calculations using simple compartment models of the Altamaha River estuary, Georgia

The residence and flushing times of an estuary are two different concepts that are often confused. Flushing time is the time required for the freshwater inflow to equal the amount of freshwater originally present in the estuary. It is specific to freshwater (or materials dissolved in it) and represents the transit time through the entire system (e.g., from head of tide to the mouth). Residence time is the average time particles take to escape the estuary. It can be calculated for any type of material and will vary depending on the starting location of the material. In the literature, the term residence time is often used to refer to the average freshwater transit time and is calculated as such. Freshwater transit time is a more precise term for a type of residence time (that of freshwater, starting from the head of the estuary), whereas residence time is a more general term that must be clarified by specifying the material and starting distribution. We explored these two mixing time scales in the context of the Altamaha River estuary, Georgia, and present a comparison of techniques for their calculation (fraction of freshwater models and variations of box models). Segmented tidal prism models, another common approach, have data requirements similar to other models but can be cumbersome to implement properly. Freshwater transit time estimates from simple steady-state box models were virtually identical to flushing times for four river-flow cases, as long as boxes were scaled appropriately to river flow, and residence time estimates from different box models were also in good agreement. Mixing time estimates from box models were incorrect when boxes were improperly scaled. Mixing time scales vary nonlinearly with river flow, so characterizing the range as well as the mean or median is important for a thorough understanding of the potential for within-estuary processing. We are now developing an improved box model that will allow the calculation of a variety of mixing time scales using simulations with daily variable river discharge.

Sheldon, J. E. and M. Alber. 2002. A comparison of residence time calculations using simple compartment models of the Altamaha River estuary, Georgia. Estuaries 25:1304-1317.

Documents

Overviews

Effects of Changing Freshwater Inflow to Estuaries: A Georgia Perspective

As humans continue to influence the quantity, timing, and quality of freshwater input to estuaries, it is becoming increasingly common for policies to be enacted that mandate the establishment of freshwater inflow criteria that will serve to preserve and protect estuarine ecosystems. This paper reviews the scientific literature describing how changes in freshwater inflow affect estuaries, proposes a conceptual model that explores the roles of scientists, citizens, politicians, and managers in the management of freshwater inflow to estuaries, and uses the model to explore the ways in which freshwater inflow is managed in a variety of estuaries. The scientific review is organized to provide an overview of the connections between freshwater inflow (in terms of the quantity, quality, and timing of water delivery), estuarine conditions (such as salinity and concentrations of dissolved and particulate material), and estuarine resources (such as the distribution and abundance of organisms), and to highlight our understanding of the causative mechanisms that underlie the relationships among these variables. The premise of the conceptual model is that the goal of estuarine freshwater inflow policy is to protect those resources and functions that we as a society value in estuaries, and that management measures use scientific information about the relationships among inflow, conditions, and resources to establish inflow standards that can meet this goal. The management approach can be inflow-based (flow is kept within some prescribed bounds under the assumption that taking too much away is bad for the resources), condition-based (inflow standards are set in order to maintain specified conditions in the estuary), or resource-based (inflow standards are set based on the requirements of specific resources), but each of these is carried out by regulating inflow. This model is used as a framework to describe the development of freshwater inflow criteria for estuaries in Texas, Florida, and California.

Merryl Alber. A Conceptual Model of Estuarine Freshwater Inflow Management. Estuaries 25(68): 1246-1261 (2002).

Freshwater Inflow: Science, Policy and Management

The papers in this special issue were presented in a special session during the 2001 biennial conference of the Estuaries Research Federation held in St. Pete Beach, Florida. This session, “Freshwater inflow: Science, policy and management,” was focused on issues related to reduced freshwater inflow to estuaries. The session brought together scientists, managers, and regulators, and included presentations on the estimation of freshwater input to estuaries, development of ecological indicators to assess changes in inflow, management strategies used to set freshwater requirements, and experiences with the reintroduction of freshwater to restore inflow.

Paul A. Montagna, Merryl Alber, Peter Doering, and Michael S. Connor. Freshwater Inflow: Science, Policy, Management. Estuaries 25(68): 1243-1245 (2002).

Water Use Patterns in the Watersheds of the Georgia Riverine Estuaries

We examined water use patterns in the hydrologic units that comprise the watersheds of the 5 major coastal rivers in Georgia (Savannah, Ogeechee, Altamaha, Satilla, St. Marys). The data for this analysis were obtained from the Georgia Water Use Program, which regularly surveys both water sources (groundwater and surface water) and water uses (domestic, commercial, industrial, mining, irrigation, livestock, thermoelectric, and hydroelectric) as part of the USGS National Water Use Synthesis. Total water withdrawal in the study area totaled 5749 million gallons per day (mgd) in 1995, with no large changes in either water withdrawal or water use patterns for the last 3 reporting years (1985, 1990, and 1995). Surface water accounted for 91% of the water withdrawal in the region, and much of this was for thermoelectric use in the watersheds of the Savannah and Altamaha Rivers. However, most of the groundwater that was withdrawn was withdrawn in the Coastal Plain. Only 10% of the water withdrawn was actually consumed, with the remainder returned to the surface water. Irrigation represented the largest consumptive use, and much of this occurred in the Coastal Plain.

Merryl Alber and Carrie Smith. 2001. Water Use Patterns in the Watersheds of the Georgia Riverine Estuaries. Proceedings of the 2001 Georgia Water Resources Conference, March 26-27, 2001, at the University of Georgia. Kathryn J. Hatcher, editor, Institute of Ecology, University of Georgia, Athens, Georgia.

Vegetation

Linking Shifts in Historic Estuarine Vegetation to Salinity Changes Using a GIS

There are anecdotal reports that upstream water withdrawals over the past 50 years have altered the salinity structure of coastal Georgia estuaries. Since few consistent salinity records exist, it may be possible to use shifts in vegetation to document salinity change. The purpose of this study was to use aerial photographs and GIS analysis to determine if the location of the brackish water interface in two Georgia estuaries has changed. Current vegetation maps of the Satilla and Altamaha estuaries were constructed from 1993 USGS DOQQs. Vegetation was outlined and classified as Juncus roemerianus, brackish marsh, fresh marsh, salt marsh, or other. Historic vegetation maps were similarly constructed from 1:77000-scale color infrared photographs taken in 1974 and 1:24000-scale black and white photographs taken in 1953. Change maps between all years were constructed for each river. In the Altamaha River, 6,786 hectares of marsh area were mapped, of which 77% did not change between 1953 and 1993. Of the 10,205 hectares of marsh area mapped in the Satilla, 87% did not change between 1953 and 1993. Shifts in Juncus constituted the primary vegetation change in both estuaries (95% in the Satilla and 87% in the Altamaha). However, these changes in Juncus do not necessarily reflect changes in estuarine salinity, indicating a need for further investigation of Juncus interactions in these systems.

Carrie Smith, Merryl Alber, and Alice Chalmers. 2001. Linking Shifts in Historic Estuarine Vegetation to Salinity Changes Using a GIS. Proceedings of the 2001 Georgia Water Resources Conference, March 26-27, 2001, University of Georgia. (ed.) Kathryn J. Hatcher.

Spartina Species Zonation Along the Altamaha River Estuary

Changes in freshwater inflow can cause changes in the distribution and diversity of marsh vegetation in estuarine habitats. In the fall of 2002 bankside vegetation was surveyed along the 24 km length of the Altamaha River estuary (n= 14 sites). Sites were quantified for multiple plant and edaphic parameters, including plant density, height, and tiller diameter. In this paper we present the characteristics of the bankside marsh vegetation as they change along the estuarine salinity gradient, and evaluate the use of a proportional relationship between two marsh grasses, Spartina cynosuroides and S. alterniflora, as a way to identify a transition line between salt and brackish marsh communities. S. alterniflora densities were greatest at the mouth of the estuary and decreased upstream and S. cynosuroides densities showed the opposite pattern, but there was not a well defined transition between these two plant communities. The percent S. cynosuroides cover along the estuary is a potentially useful way to document the response of the estuary to changing amounts of freshwater inflow.

Susan White and Merryl Alber. 2003. Spartina Species Zonation along the Altamaha River Estuary. Proceedings of the 2003 Georgia Water Resources Conference, April 23-24, 2003, University of Georgia. (ed.) Kathryn J. Hatcher.

Salinity

Comparing Transport Times through Salinity Zones in the Ogeechee and Altamaha River Estuaries Using Squeezebox

This study explored differences in the transit times of dissolved substances through salinity zones in the Altamaha and Ogeechee River estuaries under a range of flow conditions. Salinity distributions and transit times were estimated from box models generated using the SqueezeBox modeling framework. The estuaries were compared in spite of the large difference in their river flow ranges by using flow rates ranging from the 10th-90th percentile within each range. In each case, zone lengths and transit times were calculated for the tidal freshwater, oligo-mesohaline, and polyhaline zones. Although the two estuaries have similar lengths, the slower-flowing Ogeechee grades from a zone of tidal freshwater (except at very low flows) through oligo-mesohaline zones to a polyhaline zone inside the mouth whereas the Altamaha always has a fairly long (>25 km) extent of tidal freshwater but only a short (or non-existent) polyhaline zone. Transit times through the whole Ogeechee estuary are 3.3-4.7 times longer than those in the Altamaha, but the lengths of time water spends in the tidal freshwater reaches of the estuaries are comparable whereas there are large differences in the times spent in oligo-mesohaline and polyhaline reaches. These types of predictions may be useful in interpreting nutrient and pollutant dynamics in estuaries as well as in studies that compare the relative susceptibility of estuaries to perturbations.

Joan E. Sheldon and Merryl Alber. 2005. Comparing Transport Times through Salinity Zones in the Ogeechee and Altamaha River Estuaries Using Squeezebox. Proceedings of the 2005 Georgia Water Resources Conference, April 25-27, 2005, University of Georgia. (ed.) Kathryn J. Hatcher.

Salinity Response of the Satilla River Estuary to Seasonal Changes in Freshwater Discharge

Georgia’s vast brackish water landscape is maintained, to a large extent, by the hydrostatic pressure of freshwater discharges which keep the sea out of these areas. The salinity regime throughout this landscape responds to fluctuations in discharge. We describe the salinity regime in the Satilla River Estuary based on two intensive field campaigns in 1999 (20 Jan – 20 Mar and 9 Sept – 19 Oct). River discharge varied from almost 150 m3s-1 in February (twice the average) due to a single rain event in late January, to below 10 m3s-1 in May and June, after which it remained relatively low. The single discharge event resulted in large decreases in salinity throughout the estuary that lasted for about one week. (Salinity in Crows Harbor Reach was between 12-14 practical salinity units (PSU) on 20 Jan but fell to less than 2 PSU by 5 Feb) After early February, salinity slowly increased and had returned to near January levels by mid-April. Thus, during the ramp-up of river discharge in late January, the estuary flushed out much of its salt within about 20 days, and it took more than 2 months (70 days) to return to the salinity levels observed in January. The events analyzed here are described within the context of a series of salinity surveys over the course of 1999 and 2000, which should enable managers to gain insight into the interactions between river discharge, salinity structure, and flushing times in this system.

Jack Blanton, Merryl Alber, and Joan Sheldon. 2001. Salinity Response of the Satilla River Estuary to Seasonal Changes in Freshwater Discharge. Proceedings of the 2001 Georgia Water Resources Conference, March 26-27, 2001, at the University of Georgia. Kathryn J. Hatcher, editor, Institute of Ecology, University of Georgia, Athens, Georgia.

Trends in Salinities and Flushing Times of Georgia Estuaries

From 1973-1992, the Georgia EPD sponsored a monitoring program in which surface salinities were sampled regularly at fixed stations in many of Georgia’s estuaries. We used these data to examine changes in the salinities and flushing times of the Savannah, Ogeechee, Altamaha, Satilla, and St. Marys estuaries over the period of record. Water-year average salinities increased slightly over time in four of the five estuaries. When data were smoothed with a three-year moving average (based on fast Fourier analysis of river discharge), the increases in salinity were statistically significant in the Satilla and Savannah River estuaries. We used the measured salinity values to estimate flushing times (average transit time of river water through an estuary) over the period of record. Flushing times averaged 28 d in the Ogeechee, 7 d in the Altamaha, 63 d in the Satilla, and 65 d in the St. Marys, although there was considerable inter-annual variability in these estimates. These results are discussed in light of current proposals to increase surface water withdrawal from the Georgia rivers.

Merryl Alber and Joan Sheldon. 1999. Trends in Salinities and Flushing Times of Georgia Estuaries. Proceedings of the 1999 Georgia Water Resources Conference, Athens, GA (K.J. Hatcher, editor) The Institute of Ecology, Univ. of Georgia, pp.528-531.