Impact of Submerged Aquatic Vegetation on Water Quality in Cache Slough Complex, Sacramento-San Joaquin Delta: a Numerical Modeling Study

Submerged aquatic vegetation (SAV) plays a significant role in many aquatic systems, and impacts both physical and ecological quantities. It can baffle currents, attenuate waves, recycle nitrogen and phosphorus from the sediment bed, perform ecosystem function as a primary producer, and provide critical habitat for many aquatic species. Conversely, the invasive SAV, Egeria densa (Brazilian waterweed), in the San Francisco Bay & Delta has been a nuisance since its introduction into the system in the 1960s. It has displaced most of the native submersed aquatic plant species in the Delta and restructured the ecosystem, thus threatening the survival of several endangered native fishes such as Delta Smelt. Its impacts on the ecological system remain largely unknown and the need for assessment is growing. This multi-interdisciplinary study, incorporating biogeochemistry, hydrodynamics, and numerical computing and field survey data, accomplishes two main goals. The first goal is to develop a new SAV model imbedded into the unstructured-grid SCHISM-ICM framework. in addition to the advantages of directly simulating the SAV impact on hydrodynamics using high-resolution unstructured grids, this new SAV model can also simulate the competition between SAV and phytoplankton for light and nutrient supplies. The second goal is to apply the new model to Cache Slough Complex, Sacramento-San Joaquin Delta, to estimate the impact on the water quality from intervening SAV removal. Removal of SAV is already being studied in Little Hastings Tract and this study can serve to develop hypotheses for monitoring and ultimately guidance for managing SAV removal in the Bay-Delta region. We benchmark the new SAV model with the tests on the SAV biomass, growth and impacts on light supply and nutrient budget in the water column and sediment bed, respectively. Starting from a uniform biomass distribution, we simulate the evolution of biomass over seasonal scales and validate the calculated distribution with the observed distribution. The model is able to successfully simulate the SAV die-off process in areas where it is known to be unable to colonize. By applying the fully coupled SCHISM-ICM-SAV model in the Cache Slough Complex area, the changes of the water quality state variables due to SAV are estimated over spatial and seasonal scales. Generally, SAV increases the accumulation of phytoplankton by locally reducing flushing and thus increasing the residence time, but in the meantime, reduces its local growth rate due to light shading and nutrient competition. A combination of direct impact from SAV and indirect impact through changed phytoplankton results in changes in other water quality variables: dissolved oxygen and nutrients. SAV tends to increase oxygen and organic nutrients while decreasing inorganic nutrients. For this system, the feedback loop from SAV to the hydrodynamics plays the most important role in the water quality variables among all feedback loops

Some considerations on coastal processes relevant to sea level rise

The effects of potential sea level rise on the shoreline and shore environment have been briefly examined by considering the interactions between sea level rise and relevant coastal processes. These interactions have been reviewed beginning with a discussion of the need to reanalyze previous estimates of eustatic sea level rise and compaction effects in water level measurement. This is followed by considerations on sea level effects on coastal and estuarine tidal ranges, storm surge and water level response, and interaction with natural and constructed shoreline features. The desirability to reevaluate the well known Bruun Rule for estimating shoreline recession has been noted. The mechanics of ground and surface water intrusion with reference to sea level rise are then reviewed. This is followed by sedimentary processes in the estuaries including wetland response. Finally comments are included on some probable effects of sea level rise on coastal ecosystems. These interactions are complex and lead to shoreline evolution (under a sea level rise) which is highly site-specific. Models which determine shoreline change on the basis of inundation of terrestrial topography without considering relevant coastal processes are likely to lead to erroneous shoreline scenarios, particularly where the shoreline is composed of erodible sedimentary material. With some exceptions, present day knowledge of shoreline response to hydrodynamic forcing is inadequate for long-term quantitative predictions. A series of interrelated basic and applied research issues must be addressed in the coming decades to determine shoreline response to sea level change with an acceptable degree of confidence. (PDF contains 189 pages.

Progress and challenges in coupled hydrodynamic-ecological estuarine modeling

© The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Estuaries and Coasts 39 (2016): 311-332, doi:10.1007/s12237-015-0011-y.Numerical modeling has emerged over the last several decades as a widely accepted tool for investigations in environmental sciences. In estuarine research, hydrodynamic and ecological models have moved along parallel tracks with regard to complexity, refinement, computational power, and incorporation of uncertainty. Coupled hydrodynamic-ecological models have been used to assess ecosystem processes and interactions, simulate future scenarios, and evaluate remedial actions in response to eutrophication, habitat loss, and freshwater diversion. The need to couple hydrodynamic and ecological models to address research and management questions is clear because dynamic feedbacks between biotic and physical processes are critical interactions within ecosystems. In this review, we present historical and modern perspectives on estuarine hydrodynamic and ecological modeling, consider model limitations, and address aspects of model linkage, skill assessment, and complexity. We discuss the balance between spatial and temporal resolution and present examples using different spatiotemporal scales. Finally, we recommend future lines of inquiry, approaches to balance complexity and uncertainty, and model transparency and utility. It is idealistic to think we can pursue a “theory of everything” for estuarine models, but recent advances suggest that models for both scientific investigations and management applications will continue to improve in terms of realism, precision, and accuracy.NKG, ALA, and RPS acknowledge support from the USGS Coastal and Marine Geology Program. DKR gratefully acknowledges support from NSF (OCE-1314642) and NIEHS (1P50-ES021923-01). MJB and JMPV gratefully acknowledge support from NOAA NOS NCCOS (NA05NOS4781201 and NA11NOS4780043). MJB and SJL gratefully acknowledge support from the Strategic Environmental Research and Development Program—Defense Coastal/Estuarine Research Program (RC-1413 and RC-2245)

Progress and Challenges in Coupled Hydrodynamic-Ecological Estuarine Modeling

Numerical modeling has emerged over the last several decades as a widely accepted tool for investigations in environmental sciences. In estuarine research, hydrodynamic and ecological models have moved along parallel tracks with regard to complexity, refinement, computational power, and incorporation of uncertainty. Coupled hydrodynamic-ecological models have been used to assess ecosystem processes and interactions, simulate future scenarios, and evaluate remedial actions in response to eutrophication, habitat loss, and freshwater diversion. The need to couple hydrodynamic and ecological models to address research and management questions is clear because dynamic feedbacks between biotic and physical processes are critical interactions within ecosystems. In this review, we present historical and modern perspectives on estuarine hydrodynamic and ecological modeling, consider model limitations, and address aspects of model linkage, skill assessment, and complexity. We discuss the balance between spatial and temporal resolution and present examples using different spatiotemporal scales. Finally, we recommend future lines of inquiry, approaches to balance complexity and uncertainty, and model transparency and utility. It is idealistic to think we can pursue a theory of everything for estuarine models, but recent advances suggest that models for both scientific investigations and management applications will continue to improve in terms of realism, precision, and accuracy

Tracer and Timescale Methods for Passive and Reactive Transport in Fluid Flows

Geophysical, environmental, and urban fluid flows (i.e., flows developing in oceans, seas, estuaries, rivers, aquifers, reservoirs, etc.) exhibit a wide range of reactive and transport processes. Therefore, identifying key phenomena, understanding their relative importance, and establishing causal relationships between them is no trivial task. Analysis of primitive variables (e.g., velocity components, pressure, temperature, concentration) is not always conducive to the most fruitful interpretations. Examining auxiliary variables introduced for diagnostic purposes is an option worth considering. In this respect, tracer and timescale methods are proving to be very effective. Such methods can help address questions such as, "where does a fluid-born dissolved or particulate substance come from and where will it go?" or, "how fast are the transport and reaction phenomena controlling the appearance and disappearance such substances?" These issues have been dealt with since the 19th century, essentially by means of ad hoc approaches. However, over the past three decades, methods resting on solid theoretical foundations have been developed, which permit the evaluation of tracer concentrations and diagnostic timescales (age, residence/exposure time, etc.) across space and time and using numerical models and field data. This book comprises research and review articles, introducing state-of-the-art diagnostic theories and their applications to domains ranging from shallow human-made reservoirs to lakes, river networks, marine domains, and subsurface flow

The future of coastal and estuarine modeling: Findings from a workshop

This paper summarizes the findings of a workshop convened in the United States in 2018 to discuss methods in coastal and estuarine modeling and to propose key areas of research and development needed to improve their accuracy and reliability. The focus of this paper is on physical processes, and we provide an overview of the current state-of-the-art based on presentations and discussions at the meeting, which revolved around the four primary themes of parameterizations, numerical methods, in-situ and remote-sensing measurements,and high-performance computing. A primary outcome of the workshop was agreement on the need to reduce subjectivity and improve reproducibility in modeling of physical processes in the coastal ocean. Reduction of subjectivity can be accomplished through development of standards for benchmarks, grid generation, and validation, and reproducibility can be improved through development of standards for input/output, coupling and model nesting, and reporting. Subjectivity can also be reduced through more engagement with the applied mathematics and computer science communities to develop methods for robust parameter estimation anduncertainty quantification. Such engagement could be encouraged through more collaboration between thef orward and inverse modeling communities and integration of more applied math and computer science into oceanography curricula. Another outcome of the workshop was agreement on the need to develop high-resolution models that scale on advanced HPC systems to resolve, rather than parameterize, processes with horizontal scales that range between the depth and the internal Rossby deformation scale. Unsurprisingly,more research is needed on parameterizations of processes at scales smaller than the depth, includingparameterizations for drag (including bottom roughness, bedforms, vegetation and corals), wave breaking, and air–sea interactions under strong wind conditions. Other topics that require significantly more work to better parameterize include nearshore wave modeling, sediment transport modeling, and morphodynamics. Finally, it was agreed that coastal models should be considered as key infrastructure needed to support research, just like laboratory facilities, field instrumentation, and research vessels. This will require a shift in the way proposals related to coastal ocean modeling are reviewed and funded

Three-Dimensional Numerical Modeling Of Multiple-Sized Sediment Transport Modeling Under Current And Waves

In this study, a three-dimensional numerical model of multiple-sized sediment transport under current and waves is developed. The coastal circulations are described by a three-dimensional hydrodynamic model, which is governed by the three-dimensional phase-averaged shallow water flow equations coupled with wave radiation stresses. Methods are also developed to determine the bed shear stress due to current only, waves only, and coexistence of current and waves, accounting for the nonlinear interaction of the current and waves on bed shear stresses. Meanwhile, empirical formulas for bed-load transport capacity, suspended-load transport capacity, and near-bed suspended-load concentration under current and waves are established for multiple-sized sediments. These formulas are used to close the sediment transport model. The flow and sediment transport equations are solved using a finite volume method on non-staggered grid. The computational mesh is composed of quadtree rectangular grid on the horizontal plane and sigma coordinate in the vertical direction. The SIMPLEC algorithm with Rhie and Chow\u27s momentum interpolation is used to couple the flow velocity and water level. A coupled solution procedure is used to solve the discretized sediment transport, bed change and bed material sorting equations together. The empirical formulas for bed-load and suspended-load transport rates and the near-bed suspended-load concentration have been tested intensively using a large volume of single- and multiple-sized sediment transport data under current and waves. Statistics show that more than 50% of the cases are predicted within a factor of 2 of the measured values and more than 80% of the cases are within a factor of 5. The hydrodynamic model has been validated using two laboratory cases and two field cases, which demonstrate the reliability of the flow model and its coupling with wave model. The multiple-sized sediment transport sediment transport model has been validated using three laboratory cases and one field case. The predications of the model are in good agreement with the measurements. Sensitivity analyses have also been conducted for the bed friction coefficient, suspended-load scale factor, Schmidt Number, bed-load adaptation length, and roughness height constant. The developed sediment model has been demonstrated its capability of predicting morphologic behavior through the test cases

Statistical characterization of spatio-temporal sediment dynamics in the Venice lagoon

Characterizing the dynamics of suspended sediment is crucial when investigating the long-term evolution of tidal landscapes. Here we apply a widely tested mathematical model which describes the dynamics of cohesive and noncohesive sediments, driven by the combined effect of tidal currents and wind waves, using 1 year long time series of observed water levels and wind data from the Venice lagoon. The spatiotemporal evolution of the computed suspended sediment concentration (SSC) is analyzed on the basis of the \u201cpeak over threshold\u201d theory. Our analysis suggests that events characterized by high SSC can be modeled as a marked Poisson process over most of the lagoon. The interarrival time between two consecutive over threshold events, the intensity of peak excesses, and the duration are found to be exponentially distributed random variables over most of tidal flats. Our study suggests that intensity and duration of over threshold events are temporally correlated, while almost no correlation exists between interarrival times and both durations and intensities. The benthic vegetation colonizing the central southern part of the Venice lagoon is found to exert a crucial role on sediment dynamics: vegetation locally decreases the frequency of significant resuspension events by affecting patiotemporal patterns of SSCs also in adjacent areas. Spatial patterns of the mean interarrival of over threshold SSC events are found to be less heterogeneous than the corresponding patterns of mean interarrivals of over threshold bottom shear stress events because of the role of advection/dispersion processes in mixing suspended sediments within the lagoon. Implications for long-term morphodynamic modeling of tidal environments are discussed

Hydrodynamic Modeling of Lake Champlain: Current Resources, Major Gaps

Hydrodynamic models are computer-based programs designed to simulate processes and movements in water bodies. Scientists and policymakers use the robust information produced by hydrodynamic models to improve our understanding and develop policies for the protection and future management of water bodies. Current environmental issues in Lake Champlain that are or could be informed by hydrodynamic models include excess nutrients, changing temperature dynamics, flooding, harmful algae blooms, pathogens, contaminants, and invasive species. Existing hydrodynamic models are currently used to forecast flood risk and to determine how seasonal water current and nutrient dynamics affect the occurrence of harmful algae blooms, among other applications. In Lake Champlain, hydrodynamic models have been developed and utilized for a variety of purposes. This document summarizes early modeling efforts focused on Lake Champlain and describes five hydrodynamic models used to describe the hydrodynamics of the lake

Decadal-timescale estuarine geomorphic change under future scenarios of climate and sediment supply

© The Authors, 2009. This article is distributed under the terms of the Creative Commons Attribution Noncommercial License. The definitive version was published in Estuaries and Coasts 33 (2010): 15-29, doi:10.1007/s12237-009-9244-y.Future estuarine geomorphic change, in response to climate change, sea-level rise, and watershed sediment supply, may govern ecological function, navigation, and water quality. We estimated geomorphic changes in Suisun Bay, CA, under four scenarios using a tidal-timescale hydrodynamic/sediment transport model. Computational expense and data needs were reduced using the morphological hydrograph concept and the morphological acceleration factor. The four scenarios included (1) present-day conditions; (2) sea-level rise and freshwater flow changes of 2030; (3) sea-level rise and decreased watershed sediment supply of 2030; and (4) sea-level rise, freshwater flow changes, and decreased watershed sediment supply of 2030. Sea-level rise increased water levels thereby reducing wave-induced bottom shear stress and sediment redistribution during the wind-wave season. Decreased watershed sediment supply reduced net deposition within the estuary, while minor changes in freshwater flow timing and magnitude induced the smallest overall effect. In all future scenarios, net deposition in the entire estuary and in the shallowest areas did not keep pace with sea-level rise, suggesting that intertidal and wetland areas may struggle to maintain elevation. Tidal-timescale simulations using future conditions were also used to infer changes in optical depth: though sea-level rise acts to decrease mean light irradiance, decreased suspended-sediment concentrations increase irradiance, yielding small changes in optical depth. The modeling results also assisted with the development of a dimensionless estuarine geomorphic number representing the ratio of potential sediment import forces to sediment export forces; we found the number to be linearly related to relative geomorphic change in Suisun Bay. The methods implemented here are widely applicable to evaluating future scenarios of estuarine change over decadal timescales.This study was supported by the US Geological Survey’s Priority Ecosystems Science program, CALFED Bay/ Delta Program, and the University of California Center for Water Resources