Newport Back Bay Fluid Flow

Natalie Albor Alexander Holtz Alan Nguyen August 17, 2012

Abstract Water qualities including oxygen, salinity, temperature, and pH are all important qualities of estuaries and coastal systems. They are important to the many animals and aquatic species that can be found there. At the Newport Back Bay, an estuary in Southern California, the mixture of freshwater and saltwater is a delicate environment that many animals have adapted to. We monitored the fluctuations in these qualities throughout the bay using a refractometer on water samples, and also a multi-probe to collect data in the bay over several weeks. We analyzed the effect of fluid flow in the bay and how it disperses these qualities to be able to predict what effects would be seen if there were to be a change in the inflow from either the San Diego Creek (SDC) at the northern end of the estuary, or the Pacific Ocean at the southern end. Fluid flow determines the spread of freshwater and saltwater in the bay, and thus the unique estuarial results caused by this interaction.

1 Introduction the harbor. The water flow then disperses and spreads the uplifted sedi- In this study, we analyzed fluid flow of ment throughout the bay, disturbing Upper Newport Bay (UNB) and Lower the settled shellfish, plants, and fish. Newport Bay (LNB) to predict water flow patterns and dispersion of various Within the next decade, the Irvine nutrients such as salinity, pH, temper- Water Company plans on increasing ature, and dissolved oxygen. Being an the San Diego Creek (SDC) water flow estuary, UNB is a mixture of freshwa- into the UNB by ten-fold, dramatically ter and saltwater, making the fluid flow increasing the flow of freshwater into within the bay to be very important to the bay [11]. This new change of wa- the ecosystem. The salt and oxygen ter flow can affect the sensitive bivalves levels are critical to the development and other animals in their relation- and health of the aquatic animals. In ship to the habitat. There have been addition to the many fish and plants many extensive studies into the affects that prosper in the bay, there are also of decreasing the amount of freshwa- many species of bivalves that thrive in ter flow into an estuary, such as in San varying conditions of fresh and salt wa- Francisco, which clearly depicts a neg- ter. In the LNB, dredging is taking ative outcome [1]. Such results include place to allow the passage of ships to a reduction in natural nutrients and

1 shellfish populations with the intro- ability to thrive. ductory of predatory marine animals. In particular, the many species of Although there are not many studies bivalves that reside in UNB and LNB showing the effects of increasing the are essential to the health of the har- freshwater flow, it is predictable that bor. The bivalves, which include vari- there will be a negative outcome. The ous clams and oysters, mainly prey on results could include reduced salinity the millions of phytoplankton that live and die-offs of salinity sensitive plants, in the water, which controls their num- fish, and shellfish. Many of the species bers to a reasonable amount. If the bi- that reside in UNB are endangered in- valves were removed from the harbor cluding the light-footed clapper rail. due to inhabitable water conditions, With the possible change in food sup- the phytoplankton population would ply and nutrients available due to the increase beyond control, thus causing change in freshwater flow, these species eutrophication in the water [10]. This may lose their homes and become ex- will eventually lead to hypoxic condi- tinct. tions, meaning a depletion of oxygen The dredging of LNB is viewed as a in the water, which would cause the necessary action needed to allow move- other aquatic animals to lower in num- ments of ships in the bay, and it is ber. Thus, it is important to ensure believed that any negative effects it that the water in the UNB and LNB is has on the surrounding environment favorable for the bivalves. are negligible. Changes to water qual- Bivalves and other aquatic animals ity due to pollutants mixing with sedi- depend upon favorable water quality ments, and changes in sediment trans- levels of oxygen, pH, salinity, and tem- port are a couple effects known to be perature. Modeling the variations of caused by dredging [6]. The water flow these nutrients is also beneficiary to see carries and disperses the uplifted pol- any fluctuations of the nutrients based lutants and can be transferred to ar- on time, space, and fluid flow. It will eas that were previously healthy. Al- enable us to have a better understand- though LNB is not the location for ing of the environment in general, and most of the endangered species living make predictions of change in water in the bay, it is still a location for quality based on a change of saltwa- fishing and for people to take part in ter/freshwater fluid flow. water activities. The water flow dis- persement of sediments and pollutants spreads throughout the bay, hurting 2 Methods the aquatic animals and the well being of people. 2.1 The Site Modeling the bathymetry and fluid flow throughout UNB and LNB is es- The Newport Bay is located in South- sential in understanding the disperse- ern California between San Diego and ment of freshwater from the SDC and Los Angeles, and is broken up into the pollutants from dredging. This knowl- Upper Newport Bay and Lower New- edge will help predict the impact on port Bay. The UNB is classified as an the estuary and the many species that estuary because it has the freshwater of live there, ensuring their survival and the San Diego Creek flowing into it and

2 the saltwater from the Paciﬁc Ocean (through the LNB). It is about 5.5km in length and spreads about 1000 acres of total protected habitat. Since estuaries are unique combinations of fresh water and salt water, the UNB is home to many endangered species placing it in the protection of California Bays and Estuaries Policy [7].

Lower Newport Bay [2]

2.2 Modeling Equations A basic understanding of fluid flow was first needed to approach our problem. The St. Venant equations (SVE), or also known as the shallow water equations, provides a more theoretical approach to fluid flow. The SVE are a set of hyperbolic partial differential equations that describe the flow below a pressure surface in a fluid. The SVE is a combination of the continuity equation ∂A ∂V ∂h V + A + b = 0 ∂t ∂x ∂t and the dynamic, or momentum equation ∂h ∂V ∂V g + V + = g(i − j) ∂x ∂x ∂t Upper Newport Bay [4] where A is the cross-sectional area, h is the depth of flow, V is the mean ve- The LNB is the connecting harbor locity, b is the width of the top of the to UNB and the Pacific Ocean. It is a section, x is the position of the section semi-artificial harbor formed by dredg- measured from the upstream end, t is ing during the 1900s. Most of the area time, g is gravity, and ρ is the mass is covered with private homes, docks, density of the fluid. and businesses, including the two main In this form the equations cannot islands Lido Island and Balboa Island. be solved explicitly, having us use the The 39.8 square miles of LNB is con- more convenient characteristic form of stantly in need of dredging for the up- the SVE which is keep of the harbor and the 9000 boats d(v ± 2c) dx that reside there. = g(i−j) for = (v±c), dt dt

3 where c is the celerity, or speed of the a linear, first order, partial differential wave. With this method, numerical so- equation with constant coefficients. It lutions can be found. takes a function and moves it along an axis over time keeping the function in its same form.

Note that the equation simply shifts the graph

This equation is relevant to our even- tual fluid flow model of the Newport In the figure above, the graph repre- Back Bay because it mimics the tran- sents a flood wave at the upstream end sitional nature of moving water. Much of a channel. The zone of quiet repre- like how the transport equation rep- sents the part of the stream waiting for resents a certain function moving in a disturbance, or effect from a flowing the positive direction of the x-axis (dis- wave. For any point numbered on the tance), so does the Newport Back Bay graph, the velocity and celerity can be water current. We were able to solve determine numerically by the two pre- this derivation using Mathematica and vious points having direct connection created a three-dimensional Model of to it. For instance, the solutions for the transport equation. point 6 can be found using the velocity and celerity from points 3 and 5. The SVE provides a conceptual understanding for the basic introduction of fluid flow [9]. It allows us to solve numerically for specific points, but is dif- ficult to apply for a grander scale. In order to model the fluid flow within the Newport Bay, two partial differential equations were combined. These equations were the transport equation and the diffusion equation (based on Ficks Law of Diffusion). The transport equation Transport Model

∂u ∂u Unfortunately, the transport equa- = −k ∂t ∂x tion does not account for the spontane- ity of hydrogen molecules in water. For (where u is the concentration, t is time, this reason, solely using the transport x is the position, and k is a constant) is equation for our research was not an

4 option. In order to account for the ran- of u(x, 0) = const. and boundary con- dom movement of water, we incorpo- ditions of rated Ficks Law of Diffusion. u(0, t) = 0 (1) The diffusion equation which represents the river flow and ∂u ∂2u = D u(L, t) = a ∗ sin(bt) (2) ∂t ∂x (where D is the diffusion coefficient, u which represents the changing tides is concentration, x is position, and t is from the Pacific Ocean with an oscillat- time) is a partial differential equation ing function [3]. This equation is bet- describing the density dynamics in a ter suited to model water flow because material undergoing diffusion. In our it combines the forward acting motion case, our material is the water within of water with the transport term, but the Newport Back Bay. The diffu- also accounts for the dispersion of wa- sion equation was derived using the ter particles with the diffusion term. continuity equation and implies that With this equation, we see a better no matter is generated or removed. projected water flow below. Graphically, the diffusion equation depicts the distribution of a substance over a distance x.

It should be noted that the model shows a perfect distribution over distance x, which is not entirely appropri- ate for our data but is a decent place holder. Combining both the transport equation and diffusion equation we Model of the Fluid Flow have a germane partial differential In the above graph of the water flow, equation that is relevant to our re- the following is represented: Along the search. The combination of the trans- ”Distance X” axis, range is from 0 to port and diffusion equation 10, indicating the position of the San ∂u ∂u ∂2u Diego Creek to the Pacific Ocean; the = −k + D ∂t ∂x ∂x ”Time t” axis represents 4 days; and the z axis indicates the height of the (where u is concentration, t is time, k waves or water flow. From the graph is a constant, and D is the coefficient there are two peaks and two troughs of diffusion) with the initial condition per day, which shows the high and low

5 tides per day. These oscillations are of team 3 navigated into the restricted a higher values towards the ocean be- area of the top end of UNB with per- cause it is greater affected by the tides, mission from the BBSC. Each team where the San Diego Creek end is not. had about 20 plastic small sampling Although it produced a somewhat containers in which to collect water. accurate model of the The Newport At various time intervals, each team Back Bay fluid flow, there are some would take a water sample, and label limitations. Multiple factors were not it with the time and location using a included such as salinity, temperature, combination of maps and GPS. In ad- and conductivity. It is our hope that dition to the sampling done with ca- in the future we will be able to gener- noes, a fourth team rode bikes along ate a working equation that takes into the UNB trail. Samples from this team account these aspects. were taken at various locations along the waters edge, and also charted the 2.3 Data Collection locations and times. The water sampling took place from about 9 am to In order to properly model the fluid about 12 pm. Once finished, the water flow in UNB and LNB, it is impor- samples were all measured with a re- tant that we test the properties of the fractometer provided by the BBSC to water. We need to view the vary- measure salinity. ing qualities of the water to deliber- On August 7th, a team went to ate whether the water flow has effect the BBSC and used the pontoon boat upon those qualities. Unfavorable wa- to better extensively collect samples ter quality caused by the water flow of the bay. We used a multi probe will negatively affect the bivalves and called the Manta-2 Multiprobe lent to other aquatic species residing in the us by Eureka Environmental Engineer- bay. With this data we can create ing which collected data including con- models that depict the differences in ductivity, temperature, pH, and dis- the quality throughout the bay de- solved oxygen. The probe was capa- pending on time and space. ble of setting how often and for what To collect the data needed to know duration to collect data. It was also the varying levels of pH, oxygen, salin- capable of being connected directly to ity, and temperature throughout the a computer to upload the data found. bay, multiple trips were made there The sampling done on the pontoon trip to physically collect water samples for was broken up into two different ways. later analyzation. Multiple methods First, beginning at the BBSC at about and locations of water samples were 9 a.m., the probe was attached to the taken between July 19th through Au- boat and towed alongside while it was gust 13th, and with the aid of the Back submerged in the water. The probe Bay Science Center (BBSC), canoes was set to collect data every 1 minute, and a pontoon boat were made avail- and every minute we would mark our able to us. position with a GPS. This process con- On July 19th, a group of three tinued until reaching the SDC in the teams each used a canoe to travel in UNB. The second method using the the bay. Team 1 traveled to the LNB, probe began where the first method team 2 canoed within the UNB, and left off. We no longer kept the probe

6 submerged, but instead collected data ter to test the salinity, and we verified about every 1000 feet recording our that it matched the salinity of the wa- time and location. We changed the ter taken close to the BBSC with the settings of the probe to collect data ev- sampling containers. Water from the ery 2 seconds for the time we set it to same location was then taken and di- ”start” and ”stop”. At each new lo- luted, to ensure that the refractrome- cation, we lowered the probe into the ter would indicate the change in salin- water until it reached the floor of the ity. The multi-probe was connected bay, or until we ran out of tether to let to a computer and was placed in con- it down, then slowly pulling the probe trolled water before being used in the back up. The probe was collecting data bay. It correctly read and inputed data at a single point but was detecting any for the time designated, and when the change in the water based on its depth. probe would be pulled out of the wa- This process continued until about 2 ter, it immediately showed a change pm, traveling down into LNB, around in all the fields it was collecting data. both the Lido and Balboa Islands, so Thus the information accumulated was as to extensively collect data for all of the most accurate first-hand data to be Newport Bay. collected. In addition to the pontoon trip, As it turned out, we collected our the probe was used on additional days data when the weather was similar to throughout July ***th and August the other data collection days. This 13th. For these various days, cer- may sound like a trivial notion, but the tain docks were located throughout weather can have a major impact on the UNB and LNB. We attached the the water properties, especially in re- probe to the dock and submerged it gards to the percentage of oxygen. For into the water about one meter down. example, if the weather was cloudy ev- The probe would be set to collect data ery day, then the amount of sunlight about every 5 minutes for the duration reaching the water would be decreased. of 24 to 48 hours. The locations of the Thus, the phytoplankton that depend docks included Hill’s Boat Service in on the sunlight for photosynthesis will LNB, Pearson’s Point in lower UNB, die and diminish the amount of oxygen a buoy in UNB, and a couple other that the phytoplankton produce over- locations spread throughout the bay. all [5]. Fortunately for us, it was sunny The overnight data collection would al- most days we collected research, so if low for comparison of different loca- there was a decrease in oxygen levels tions with more time and space param- in our collected data, we know that it eters. Compared to the other meth- does not have to do with variable fac- ods of data collecting with the probe, tors such as the weather. the overnight method provided data on different values caused by the change 2.4 Data Results from day to night, and also from the tides. Once we finished collecting our data, Multiple comparisons were made to we proceeded to upload and analyze verify the data collected was accurate. the data at UC Irvine at the Center for Water was taken from the dock of the Complex Biological Systems. There BBSC and we used the refractrome- we connected the probe’s PDA to the

7 computer and it automatically up- data from the center of the channel be- loaded a spreadsheet with all the data cause it would better reflect the effects it collected, including the pH, con- of the fluid flow, and we wanted to be ductivity, oxygen, temperature, depth, able to more accurately compare the and time. Below is a small sample of changes from UNB to LNB. A chart the collected data. was made indicating the temperature, conductivity, pH, and dissolved oxygen according to the sites on the map.

With this data, multiple charts, maps, and graphs were put together to show the variations, if any. First, to have a general scope of where exactly our data was taken, a map with increasing numbers indicate the general pathway and sites we took.

With this data, we were able to generate graphs reﬂecting the change The majority of the data collecting in water quality from the SDC moving sites were taken in the center of the south towards the Paciﬁc Ocean. In bay, and a few were taken closer to the each graph the x-axis represents the in- side of the channel. We wanted more dex, or the site number marked on the

8 map. The following were the graphs generated:

The pH levels is seen to ﬂuctuate as the sites move closer to the Paciﬁc Ocean, which could be due to the greater interaction of freshwater and tidal saltwater in the LNB.

In the above graph it is seen that the dissolved oxygen remains fairly stable from the UNB to the LNB.

Temperature as well remains fairly stable throughout the bay, with only mi- nor temperature increase towards the Pacific Ocean. This may be caused by the Lido and Balboa Islands in Conductivity doesn’t measure the LNB, which may slow the water flow. amount of salt in the water directly. Whereas UNB has no major land ob- Conductivity measures how easily elec- jects like islands to impede the speed tricity can pass through the water. of the flow. Thereby the water is con- Since salt water is a better conductor stantly moving unable to keep the heat than freshwater, the higher the con- as well as the flow in the LNB does. ductivity, the larger amount of salt is

9 present in the water. The variations of conductivity is very apparent in the two graphs shown above. The first figure shows the conductivity taken by the probe at a “No Entry Sign” in the uppermost part of UNB, and has about an average conductivity of 45500. The second graph shows the conductivity at a boat service center in the LNB fairly close to the Pacific Ocean which has about an average conductivity of 47700. These graphs reflect our predictions that the salinity of the water will increase as we move closer the Pa- cific Ocean.

3 Software Another similar program lent to us by 3.1 ELCOM and CAEDYM the Centre for Water Research was the Computational Aquatic Ecosystem Dy- In order to properly model the New- namics Model (CAEDYM), which fo- port Back Bay, we needed a software cuses more on the ecological studies of that would be able to use the spe- a given environment. cific data from the bay, including the In order to run simulations in ei- floor of the bay, so that we would be ther ELCOM or CAEDYM, the user able to predict any changes that the application Aquatic Realtime Manage- flow of water may have on the sur- ment System (ARMS) was also ac- rounding environment. Fortunately, quired from the Centre for Water Re- Dr. Felix Grün(UCI Cell and Devel- search. ARMS reads the bathymetry opmental Biology) was able to acquire data (which is in the format of rows a software from the Centre for Water of numbers) and converts it to a user- Research, based in Western Australia, friendly map that is color coded to that has the capability to meet all of show the depth of the bay at a cer- our goals. This software, entitled Es- tain point. It is also possible to edit tuary, Lake and Costal Ocean Model the bathymetry data through ARMS (ELCOM) uses bathymetry data and as opposed to trying to edit the lines of boundary conditions in order to pre- code that ELCOM is dependent upon. dict the the hydrological changes in a Unfortunately, due to time con- given aquatic environment. Our group straints and the complexity of under- generated a bathymetry model using standing how the program works, we data gathered from Resource Manage- were not able to model Newport Bay ment Associates, Inc. (RMA) when using these programs as we intended. conducting a water quality study in Various errors did not allow us to ef- 2008 [8]. fectively use the program in the time

10 frame given, especially considering we ations with a greater change in flow of did not successfully install the program water for from either the SDC or Pa- until halfway through the research. cific Ocean. This can be modeled with further testing and utilization of EL- COM and CAEDYM, which we hope 4 Conclusions and to use to model the UNB using the Future Work given bathymetry data. To be able to make better models The freshwater and saltwater mixture and graphs, we wish to continue col- of the Newport Back Bay estuary is lecting data of the bay over a longer a unique, delicate environment, reliant period of time. For instance collecting upon the water flow to distribute the data during the spring months will pro- nutrients. The conductivity and salin- vide data of a higher freshwater inflow ity distribution throughout the bay is from the SDC with rainfall and moun- of vital importance, which is highly tain runoff. We plan on uploading all fluctuant from the UNB to the LNB. this data into our modeling software The bay’s inflows of water from the to generate better models and movies SDC and the Pacific Ocean need to be depicting the fluctuations of nutrients monitored to ensure the survival of an- over time, as well as the water flow imals that have adapted to the vary- throughout the same given period to ing water quality distribution through make correlations. These models can the bay. The variations of pH, oxy- then be distributed to the Back Bay gen, and temperature are also of im- Science Center and commercial indus- portance to the ecosystem of the bay, tries for their use and protection of the but may be seen to have greater vari- Newport Back Bay.

References

[1] Merryl Alber. A conceptual model of estuarine freshwater inﬂow management. Estuaries, 2002.

[2] Makai Promotions. Map of Lower Newport Bay, 2008. http://www. sailorschoice.com/NewportHarbor/nmap.htm. [3] MathWorks. Solve initial-boundary value problems for parabolic-elliptic PDEs in 1-D. http://www.mathworks.com/help/techdoc/ref/pdepe.html.

[4] Newport Bay Conservancy. Map of Upper Newport Bay, 2012. http: //newportbay.org/the-bay/habitats/high-tide-habitat-map. [5] Nikolay P. Nezlin, Kista Kamer, Jim Hyde, and Eric D. Stein. Dissolved oxygen dynamics in a eutrophic estuary, upper newport bay, california. Estuarine, Coastal, and Shelf Science, 2009.

[6] Stephen B. Olsen, Tiruponithura V. Padma, and Brian D. Richter. Man- aging Freshwater Inﬂows to Estuaries: A Methods Guide. S. Agency for International Development.

11 [7] Orange County Regional Parks. Upper Newport Bay Nature Preserve, 2008. http://www.ocparks.com/uppernewportbay/. [8] Resource Management Associates, Inc. Upper Newport Bay Water Quality Developent, November 2008.

[9] P A Sleigh and I M Goodwill. The St. Venant Equations. University of Leeds, March 2000. [10] University of Wisconsin, Green Bay. Dissolved Oxygen. http://www.uwgb.edu/watershed/data/monitoring/oxygen.htm. [11] U.S. Army Corps of Engineers, Los Angeles District, Regulatory Division and California Department of Fish and Game, Habitat Conservation South Coast Region, San Diego, California. A Special Area Management Plan (SAMP) for the San Diego Creek Watershed Orange County, California, February 2009.