Riparian floodplains and forests are simultaneously among the planet's most biodiverse and anthropogenically altered ecosystems. With 90% or more of global riparian corridors lost to development or cultivation, it is unsurprising that ecological restoration has become a multi-billion-dollar global industry. Unfortunately, many of the restoration treatment actions commonly deployed are implemented without a scientific foundation and/or lack long-term monitoring with specified success metrics. With the continued decline of global biodiversity and increasing climate volatility, a better understanding of restoration treatment outcomes is required to achieve desired long-term ecological objectives. In the absence of long-term monitoring, direct treatment comparisons, or consistent treatment methods, restoration ecologists and other decision-makers lack the fundamental tools necessary to choose the best restoration treatment. Similarly, scientists and practitioners cannot learn from failed or successful restoration treatments without long-term monitoring.In this dissertation, 40 years of restoration treatments along the Cosumnes River, CA are evaluated for a selection of ecosystem services. Chapter 1 introduces the research conducted in subsequent chapters, provides historical information about the study area, and contextualizes the objectives within a broader context. Chapter 2 assesses the geomorphic response to hydrologically reconnecting a riparian floodplain to the Cosumnes River, the largest river on the western slope of the Sierra Nevada without a major dam project. Chapter 3 details the woody species richness, diversity, and standing biomass within riparian forests. Chapter 4 documents the quantification of carbon stocks in the upper layer of soil, litter cover, and aboveground biomass in woody species across 23 different treatments, and Chapter 5 summarizes results and potential future directions. This work, conducted within the Cosumnes River Preserve, is the latest in a series of investigations that have been ongoing for more than 30 years. The dozens of restoration treatments evaluated in each chapter were consistently grouped by treatment type throughout. Treatment types include Process-based, limited intervention; Assisted, horticultural planting and other intensive restoration activities; Hybrid, a combination of process and assisted actions; and Remnant, old-growth forests that were not created with restoration actions. Results from a levee manipulation and related restoration actions in Chapter 2 include more than 25,000 m3 of sediment deposition within the original excavation site, the development of multiple sandsplays, and natural recruitment of native riparian tree species. Chapter 3 provides evidence supporting multi-benefit Process-based restoration approaches based on measurable richness and biomass following natural species establishment. Compared to the uniform species coverage of planted Assisted restoration treatment type plots, sites where flood regime reconnection has facilitated riparian floodplain functionality recruit more species and accrue more biomass. The Carbon stock quantification documented in Chapter 4 resulted in total C values of up to 1099.5 Mg ha-1 with biomass contributing the most to individual plot measurements. Biomass C stock measurements showed an average 32 Mg ha-1 increase in C present in less than a decade. Where hydrologic regimes allow, Process-based restoration approaches that restore functionality within the system allow for sediment accretion, native species recruitment, higher woody species richness, and more carbon stock accumulation. Initiatives, such as Engineering With Nature, Nature-based Solutions, and multi-benefit solutions, that utilize the ecosystem services facilitated by natural infrastructure resulting from process-based restoration can allow for disaster mitigation, ecological functionality, and resilience in surrounding communities in an increasingly volatile climate.

Different activities utilize water resources at different rates, rely on different water sources, and thus have a different “footprint” in regard to their water demand. However, the water footprint of these activities differs depending on the region and the time when the activity occurs. In popular literature, the footprint metric has seen some success in the ability to represent the large magnitude of human resource consumption, to more relatable per-capita quantities. However, these depictions are often based on global surveys that mask regional variability in water use. This thesis presents a framework for agricultural water footprint assessment, implemented using free and open source software. It explores the variability of the water footprint of select agricultural activities in the State of California from 2008 through 2015. The results describe a diverse landscape of water use variability driven primarily by crop choice. The study reveals that crop specific water footprints can have significant, inter-annual variability, independent of climatic conditions. Supported by water distribution infrastructure, agricultural activities can be found across the state. Water footprint assessments can be used by growers and resource managers, who wish to maximize utility per unit of water allocated, planners who wish to understand national risks and strengths, or the informed citizen who wishes to evaluate the sustainability of their consumptive activities.

The construction and operation of dams, reservoirs, hydropower plants, and water diversion infrastructure has significantly altered riverine ecosystems by disrupting natural hydrologic, geomorphic and ecological processes. These facilities release environmental flows to prevent and mitigate their negative impacts. Environmental flows implementation has advanced in recent decades through the development of the functional flows and active management paradigms, as well as an increasing emphasis on responsiveness to hydroclimatic variability. In order to facilitate the adoption of these modern approaches, this study establishes a baseline understanding of the extent to which these principles are currently being utilized, as well as the attitudes of facility operators regarding this topic. An online survey is used to solicit information from operators of hydropower facilities in the Western United States. We received 63 valid responses from 447 emailed survey invitations, yielding a 14 percent completed response rate. Descriptive and exploratory data analysis techniques were used to obtain insights. Results indicate that the regulatory framework and objectives for environmental flows are grounded in the protection of targeted species, especially fish. Respondents report widespread usage of traditional environmental flows techniques that are simple, static, non-collaborative, and reactive. The application of modern advances in environmental flows may be hindered by inadequate stakeholder consultation, infrastructure, and regulatory frameworks, as well as pressure to deliver for competing operational objectives (especially hydropower) after satisfying the minimum environmental regulatory requirements. Operators indicate general belief in climate change and approval towards current environmental flows regimes, yet a significant minority do not conceptualize climate change as impacting their local region or their ability to implement environmental flows in the future. Lastly, hydrologic basin and facility size may have associative relationships with the extent of environmental flows implementation. This study contributes to the body of interdisciplinary knowledge that aims to guide the siting and reoperation of river facilities for optimized ecosystem health, hydropower, and other benefits.

Global food security is a rapidly emerging concern with climate change and increasing population growth. This dissertation research assessed components critical to inform the strategic transition of irrigated agricultural lands to meet policy targets and sustain food-energy-water systems worldwide by focusing on the San Joaquin Valley, California. This region is not only a global leader in the agricultural sector but is an exemplary representation of regions facing water stress, population growth, and environmental injustice. It is also amidst its trials and tribulations regarding sustainable water policy and management. The newly implemented Sustainable Groundwater Management Act (SGMA) establishes targets for groundwater utilization to address reduced surface water supply and groundwater overdraft. In the San Joaquin Valley, more than 10-15% of irrigated agricultural land is projected to go out of production within the next 10 to 20 years to sustain California’s water supplies (Hanak et al., 2017). However, a significant question addressed in this project is how we transition agricultural land to address groundwater overdraft and minimize socioeconomic and environmental impacts on disenfranchised and underserved communities and farmers. While this reduction in irrigated acreage will help lessen groundwater overdraft as per SGMA, the reduction will also result in socioeconomic and environmental impacts on disadvantaged communities and marginalized farmers that rely on agriculture for their livelihood. The dynamics between land use and the direct and indirect implications of agricultural land use transitions remain unknown. The components of this dissertation aim to minimize the impacts of agricultural land use transitions under SGMA to those most impacted and often left out of the water and land use decisions—underserved communities and farmers. This doctoral dissertation has the following objectives:1) Identify San Joaquin Valley community land use preferences. 2) Assess irrigation district overdependence on groundwater to identify where to focus agricultural land use transition efforts. 3) Identify which land use classification datasets are best to use to assess how and where to transition agricultural land and quantify the crop revenue, crop water requirement, and GHG emission discrepancies due to misclassifications.

Quantifying terrestrial carbon (C) stocks in vineyards represents an important opportunity for estimating C sequestration in perennial cropping systems. Considering ~230,000 ha in California (8.2% of total land cultivated in CA) are dedicated to wine grape production, annual C capture and storage in woody biomass is substantial. In this study, destructive sampling was used to measure C stocks in the woody biomass of a 15-year-old Cabernet Sauvignon vines from a California Northern San Joaquin Valley vineyard. The objectives were to characterize C stocks in terms of allometric variation between biomass fractions of roots, aboveground wood, canes, leaves and fruit, and then test correlations between easy-to-measure variables such as trunk diameter, pruning weights and harvest index to vine biomass fractions. Carbon stocks were also estimated from the volume of biomass in mounds generated during vineyard removal, and compared with previous estimates of standing biomass.

Total vine C was estimated at 12.3 Mg C/ha, of which 8.9 Mg C/ha came from perennial vine biomass, whereas annual biomass was estimated at 1.7 Mg C/ha from leaves and canes and 1.7 Mg C/ha from fruit. High positive correlations were found between the diameter of the trunk and overall woody C stocks (r2 = 0.84), pruning weights and annual C stocks (r2 = 0.93), and between fruit weight and annual C stocks (r2 = 0.95). Carbon estimates in the mounds of vine biomass fractions wood, root and canes (10.25 Mg C/ha) were not significantly different than for individually measured vines (10.02 Mg C/ha).

This research demonstrates that allometric equations represent strong predictive power for C estimations due to high correlations and low error between these simple measurements and C stocks. Such equations, using information collected from vineyard management practices, could enable growers to estimate C stocks more easily and would facilitate managing C at a vineyard level. This might also provide the basis to calculate future C stock estimations, especially important considering the significance that C sequestration is taking in the production function of agro-ecosystems.

Natural floodplain ecosystems are adapted to highly variable hydrologic regimes, which include periodic droughts, infrequent large floods, and relatively frequent periods of inundation. To more effectively manage water resources and maintain ecosystem services provided by floodplains – and associated aquatic, riparian, and wetland habitats – requires an understanding of seasonal and inter-annual hydrologic variability of floodplains. The Cosumnes River, the largest river on the west-slope Sierra Nevada mountains without a major dam, provides a pertinent test case to develop a systematic classification of hydrologic variability. By examining the dynamics of its relatively natural flow regime, and a 98-year streamflow record (1908 – 2005), we identified 12 potential flood types. We identified four duration thresholds, defined as short (S), medium (M), long (L), and very long (V). We then intersected the flood duration division by three magnitude classes, defined as small-medium (1), large (2), and very large (3). Of the 12 possible flood types created by this classification matrix, the Cosumnes River streamflow record populated 10 such classes. To assess the robustness of our classification, we employed discriminant analysis to test class fidelity based on independent measures of flood capability, such as start date. Lastly, we used hierarchical divisive clustering to classify water years by flood type composition resulting in 8 water year types. The results of this work highlight the significant seasonal and inter-annual variability in natural flood regimes in Central Valley rivers. The construction of water impoundment and flood control structures has significantly altered all aspects of the flood pulse. Restoring floodplain ecosystem services will require re-establishing key elements of these historic flood regimes in order to achieve regional restoration goals and objectives.

Vernal pool landscapes are rare and highly modified. The Merced Vernal Pools and Grassland Reserve consists of 6,500 protected acres, preserving sensitive vernal pool habitat and organisms. The Reserve contains a number of modified stock ponds that have caused extensive alteration of the historic landscape to capture and retain water for longer periods than the seasonal wetland complexes dispersed throughout the site. Using a combination of empirical data and 2D hydrodynamic modeling, our project seeks to better understand how water moves throughout the UC Merced Vernal Pools and Grassland Reserve in order to evaluate the feasibility of potential hydrological restoration activities and develop a better understanding of potential management strategies. This study aims to assess the feasibility of restoring or enhancing existing natural vernal pool complexes through increased inundation by reconnecting historical channels via small alterations in previously modified terrain.

A 2D hydrodynamic model was developed using HEC-RAS rain-on-grid methodology to assess the restorative potential of a vernal pool complex at Avocet Pond in the Merced Vernal Pools and Grassland Reserve. In this currently modified system, levees disconnect natural channels and reroute overland flows into the stock pond which behaves as a reservoir, removing water from downstream landscape processes. Increased inundation to natural habitats benefits native vernal pool species whose life histories are integrally tied to finite and variable hydroperiods. Invasive plant and animal species may be reduced through the reduction of perennial stock pond hydroperiods and increased inundation and hydrologic connectivity of wetland features. Base case hydroecological conditions were established as the formative basis for evaluating the benefit of various restoration scenarios. Proposed restoration scenarios implemented simple terrain modifications such as small breaks in conveyance levees or notching stock pond berms. Model simulations suggest that historical flow paths can be reconnected through minimal terrain alteration resulting in increased inundation to wetlands and other downstream environments and reduction of overall stock pond inflows and hydroperiod. Results of this study will serve as a demonstration of landscape scale restoration of a vernal pool grassland habitat that has been altered through past land uses so that similar restoration assessment methodology can be implemented on other preserved lands in the state.

Decisions on water allocation to humans and the environment depend on physical engineering structures, various operations and allocation policies, supplies, and demands of numerous end-users. Different assumptions of current and future scenarios can anticipate decisions that best meet human and environmental objectives, under different stressors (e.g., climate change, increased demands). Environmental water allocation especially presents intricate challenges, given the interplay of various regulations and the complexities of managing water resources across different regions. Therefore, the goal of this collection of studies is to provide new insights on reservoir operations, hydropower generation and water management in the Central Sierra Nevada, California, aiming to balance human demands, while achieving greater environmental benefits. This work involves the use of a novel method for water-power modeling with a specific application to the Central Sierra Nevada, California introduced in Chapter 1, and used in Chapters 2 and 4. The modeling framework includes more detailed and facility-specific information to provide a more comprehensive and finer temporal resolution (daily time-step) of water allocation decisions than those found in most modeling efforts. This is a potentially crucial method for modeling water management, due to the reconciliation of water and power systems through the integration of hydroeconomic needs (e.g., hydropower operations) and rule-based simulation (e.g., instream flow requirements), which is one of the biggest challenges in modeling water systems. Better representation of real-world systems is essential to address the difficulties in water management and to analyze solutions. These models are made available for use in a broad range of scenario analyses, including different hydrological inputs (historical and future climates), electricity prices, and a variety of management objectives. Chapter 2 delves into the nuanced landscape of environmental flow (e-flows) requirements, primarily anchored on water year types (WYTs), to understand the efficacy and adaptability of current strategies. Through an extensive examination of pertinent hydropower licensing documents, the research identifies a lack of standardized adoption of WYTs in many river reaches, manifesting as minimal variation across different year types and limited seasonal fluctuations. Incorporating climate change projections from multiple Global Circulations Models, the study reveals significant variability in WYT distributions under existing management strategies. This variability has led to inconsistencies in e-flow management, exacerbating potential conflicts among stakeholders. To address these challenges, an adaptive strategy is proposed, employing a method to recalibrate WYT thresholds, aiming to bolster the reliability and resilience of e-flows. As a result, Chapter 3 critically analyzes the systemic barriers hindering the effective implementation of e-flows. A comprehensive systematic review and bibliometric analysis were conducted, yielding insights into the major impediments such as competing priorities of human water uses, data deficiencies, and resource and capacity limitations. To enhance the successful implementation of e-flows, the dissertation recommends a system analysis approach, utilizing modeling tools to navigate competing demands and foster holistic flow allocations based on hydroecological principles. In turn, Chapter 4 evaluates the resilience of water systems and hydropower against climate whiplash. Through 200 synthetic hydrologic sequences of different lengths of dry-wet-dry combinations, the research underscores the vulnerability of water storage and the implications for water resource management, offering policy suggestions to enhance system flexibility and resilience against climatic shocks. Finally, Chapter 5 concludes by providing policy insights and recommendations based on these studies to help inform stakeholders and decision-makers in the search for sustainable solutions to water management problems.