Local human impacts and climate change are presenting freshwater species around the world with conditions that are more extreme than those to which they evolved. Human water use and increasing drought severity are causing unprecedented low stream flow and warm water. Consequently, cold-water, migratory fish, such as salmon and steelhead trout (Oncorhynchus spp.), face challenges in completing their life cycles. As Pacific salmon navigate extensive river networks during their migration, individual fish often cannot avoid heavily impaired reaches of streams and rivers, particularly in California, USA. Salmon in the southern extent of their range already experience conditions that approach or exceed their tolerance limits. Yet, we have an incomplete understanding of flow and temperature conditions required to complete their life cycles and sustain healthy populations. Are salmon approaching thresholds in low flows, minimum depths, and maximum temperatures? How do streamflow and temperature influence the critical timing of downstream migration (outmigration) of juveniles? Do minimum thresholds exist in stream water depths that salmon can navigate? How do additional environmental and ecological stressors interact with water temperature to affect physiological thermal limits of salmon?

In this dissertation, I explore how an endangered population of coho salmon (Oncorhynchus kisutch) near the southern extent of the species range in the agricultural Russian River watershed is affected by receding streams and warming waters. In Chapter 1 we tracked outmigration of individually marked juveniles in 7 streams over 13 years, which included an historic drought with extreme dry and warm conditions. We discovered that low-flow years during droughts contracted the outmigration window by 31% (from 11 to 7 weeks), while warm years hastened the outmigration window by approximately three weeks. In Chapter 2 we investigated minimum depth thresholds for migration by applying a novel use of water depth measurements at the riffle crest thalweg, which is the shallowest repeating geomorphic feature that salmon must navigate. We found that steep reductions and a cessation in movement occur at shallow depths, but that movement-depth thresholds varied among streams with different geomorphologies. Finally, in Chapter 3 we develop a framework to assess the degree to which thermal tolerance may be reduced by ecological stressor interactions. Our example assessment demonstrates that temperature-stressor interactions, such as temperature interactions with predation, competition, and disease, may cause uneven distributions of impacts, such as development, growth and carrying capacity, to salmon populations.

Together, the chapters of this dissertation offer insights to better understand, manage, and mitigate the adverse impacts of low flow, shallow water, and warm water in salmon-bearing streams in coastal California. Our findings suggest that maintaining adequate streamflows from March through June is critical to preserving an outmigration window that is sufficiently long in duration to reduce risks of phenological mismatches when juvenile salmon reach the ocean to feed. Policies that set minimum water depth limits are likely needed in many of California’s impaired streams to protect the salmon movement during the outmigration period. This research also underscores the importance of temperature-stressor interactions when considering the potential impacts of warming waters on salmonids. The assessment framework that we introduce can serve in any salmon-bearing system to categorize temperature-stressor interactions and the potential severity of their impacts on a salmon population. Collectively, the site-specific assessment methods and findings of this dissertation can be utilized to inform strategic instream flow policies, ecological stressor reduction, and thermal criteria development. If implemented, these solutions can reduce adverse impacts of human water use and drought on endangered migratory salmon individuals and enhance the resilience of salmon populations in a changing climate.

Rivers act as dynamic forces that shape Earth’s changing surface, and whose scars we can still see punctuating our landscapes. Characteristically everchanging, they have inspired many poets, thinkers, and wanderers with their mutable nature. The quote “no man steps in the same river twice, for it is not the same river and he is not the same man” – attributed to the Ancient Greek philosopher Heraclitus – is known to be true for anyone who has seen a river swell beyond its banks, only to watch it shrink back to a narrow passage. But what about the streams that dry? The temporary, the seasonal, the irregular, the ephemeral, the discontinuous? These waterways, termed in this dissertation as ‘intermittent’, periodically, and naturally, cease to flow. They are similarly unpredictable, where the patterns and extent of drying are highly variable, with some reaches going dry year after year, regardless of previous conditions, while others respond more proportionally to the amount of antecedent rainfall. While riverine theory and study has been traditionally based on perennial model systems, recognition of the importance of intermittent streams has grown in recent years. However, critical gaps remain around the causes and consequences of intermittent stream drying across space and time. These systems are especially sensitive to climate fluctuations, and there is considerable potential for such ecosystems, and the species and services they support, to shift in response to climate change. Yet, relatively little attention has been given to identifying and evaluating the factors that influence variability in intermittent stream drying. Without documenting how intermittent streams vary within and across years, an essential component of their character is lost. With increasing precipitation volatility and rising temperatures, there is an urgent need to characterize where and when intermittent streams will be buffered from, or vulnerable to, altered climate conditions. In this dissertation, I explore the causes and consequences of intermittent stream variability, with a focus on the interannual variation in the hydrological and ecological patterns within these systems. These themes are explored at multiple scales, from the watershed to the stream reach, in three core chapters. I first evaluate the challenges and opportunities of monitoring intermittent streams in Chapter 1, before moving to understanding the controls on wetted channel extent and variability in Chapter 2, to finally characterizing the shifting habitat mosaic in Chapter 3. These three chapters together illustrate the importance of intermittent streams in shaping the environments they flow (and cease to flow) through, and underscore the need to capture the patterns of drying across space and time.

This dissertation addresses the complex relationships between human water demands and ecosystem water needs in the Mediterranean-climate region of northern California. Through a combination of long-term ecological data analysis, hydrologic modeling, and field studies of ecological-flow relationships, the research presented examines the challenges and opportunities for managing water to sustain freshwater ecosystems, with a particular emphasis on the environmental flow requirements of steelhead trout (Oncorhynchus mykiss). In coastal California watersheds, stream flows are increasingly impacted by small-scale withdrawals from agriculture and residential water users. While the effects of large dams have been extensively-studied, relatively little is known about the cumulative impacts of small-scale water-management practices on freshwater ecosystems. Analysis of a long-term record of fish count data revealed a strong positive relationship between stream flow and the over-summer survival of juvenile salmon and provided evidence that insufficient stream flows during the spring and summer rearing period has become an important limiting factor to threatened steelhead trout populations. These finding suggest that changes in water use practices that maintain dry season flows are critical for salmon population recovery.

A reduction in dry season water diversions could potentially be achieved by increasing local storage capacity in ponds, which could be filled during the wet season when there is greater water availability. However, increased water storage has the potential to impair winter flows, which are important for fish passage and spawning and the maintenance of habitat heterogeneity. To quantify the trade-offs between alternative water management strategies, an integrated management framework is introduced that simultaneously considers the temporal and spatial dynamics of flow regimes, and the water needs of both human and natural systems. The management framework relies on a watershed hydrologic routing model, which is useful for representing the temporal and spatial distribution of water availability and predicting the impacts of water diversions across the stream network. An examination of the potential impacts of water management practices in a Sonoma County, California watershed demonstrated that the location and size of water storage projects influences the magnitude and duration of stream flow impacts. The findings also illustrated trade-offs between environmental flow protections and the ability for water users to meet storage demands.

Managing stream flows for ecological benefits requires an understanding of flow-habitat relationships at scales relevant to individual organisms. To assess the flow needs of adult salmon for their upstream migration, a new approach was developed for mapping stream channel topography and modeling flows in relation to fish passage suitability. The approach relies on high-resolution measurements of stream channel topography derived from terrestrial LiDAR surveys. A two-dimensional hydraulic model was then used to simulate flows in several survey reaches and identify the minimum flow required to maintain a continuous migration path of suitable passage depths for adult salmon. The modeling approach is compared to a regional formula used by State of California resource agencies to estimate salmon passage flow needs. While the results were similar, improvements to State's regional formula could be made by explicitly incorporating a variable describing channel typology.

In sum, these studies quantify the response of a threatened salmon species to flow variation, illustrate the relationships between water management and ecologically-important flow dynamics, and establish a new approach for evaluating biological flow thresholds, all of which are critical for improving the management of freshwater ecosystems in Mediterranean-climate regions.

Habitat heterogeneity, defined by spatial variation in local environmental conditions, fosters variation in organism traits and life history strategies, which in turn can stabilize populations by buffering against climate fluctuations. In Pacific salmon (Oncorhynchus spp.), large watersheds with intact habitats support commercially, ecologically, and culturally important populations by generating a variety of life history strategies that contribute to population stability and resilience. However, habitat loss and modification have homogenized river networks inhabited by salmon, diminishing intraspecific diversity and its stabilizing effects. In systems with highly modified habitats, it is unclear whether the processes that generate intraspecific diversity are still intact. Furthermore, it is yet to be explored what level of population diversity is sufficient to ensure the survival and stability of small, imperiled populations, especially those experiencing increasingly extreme environmental conditions. This dissertation addresses these knowledge gaps by exploring the relationship between habitat diversity and population diversity within modified habitats of an endangered salmon population complex, aiming to understand its resilience amidst increasingly variable environmental conditions. I focus on a population of critically endangered Central California Coast coho salmon (O. kisutch) in the Lagunitas Creek watershed in Marin County, California as a case study of an imperiled population in a small watershed at the southern edge of the species’ range experiencing effects of climate change. In Chapter 1, I examine how diverse habitats across the watershed differentially filter extreme drought conditions and the consequences for juvenile coho persistence, foraging behavior, and growth opportunities. Building on observed variation in juvenile traits during a summer of drought in Chapter 1, I assess diversity in long-term juvenile subpopulation dynamics across the region and the effects of seasonal flow conditions in Chapter 2. In Chapter 3, I explore trait variation at the adult stage, leveraging monitoring data and isotopic analysis of fish ear stones to characterize spawning distributions in space and time in relationship to winter hydrology. Spawning dispersal data also revealed key habitats that support returning adults. Findings from all three chapters highlight the importance of habitat diversity and connectivity for population persistence amidst environmental variability and disturbance. By better understanding the underlying dynamics of an endangered population, we can better assess vulnerability to extirpation and create targeted restoration actions to enhance population resilience.

Management of California's vast water distribution network, involving hundreds of dams and diversions from rivers and streams, provides water to 40 million people and supports a globally prominent agricultural sector, but it has come at a price to local freshwater ecosystems. An essential first step in developing policies that effectively balance human and ecosystem needs is understanding natural stream flow patterns and the role stream flow plays in supporting ecosystem health. We have developed a machine-learning modeling technique that predicts natural stream flows in California's rivers and streams. The technique has been used to assess patterns of stream flow modification, evaluate statewide water rights allocations and establish environmental flow thresholds below which water diversions are prohibited. Our work has informed the statewide Cannabis Cultivation Policy and influenced decision-making in more subtle ways, such as by highlighting shortcomings in the state's water accounting system and building support for needed reforms. Tools and techniques that make use of long-term environmental monitoring data and modern computing power — such as the models described here — can help inform policies seeking to protect the environment while satisfying the demands of California's growing population.

Water use by cannabis cultivators represents an emerging threat to surface flows in Northern California's sensitive watersheds. To date, however, no data has been available to formally assess where cannabis sites source their water. This study analyzed data from annual reports, covering the year 2017, submitted by 901 cannabis cultivators enrolled in the Cannabis Waste Discharge Regulatory Program administered by the North Coast Regional Water Quality Control Board. The analysis identified cannabis cultivators' most common sources for water extraction, monthly patterns for each water source and differences between sites compliant and not compliant with the cannabis program. The most commonly reported source of water was wells (58% of sites), with most extraction from wells occurring during the growing season (April through October). Surface water diversions (22% of sites) and spring diversions (16% of sites) were the most common sources after wells, with extractions from these sources distributed much more evenly across the year. Although nearly one-third of noncompliant sites (33%) used wells, this source was more than twice as frequently reported among compliant sites (68%), indicating that wells may become increasingly common as more sites become part of the regulated cannabis industry.

Legalization of cannabis production has daylighted a unique and highly valuable crop in California agriculture. State and regulatory agencies must now address the ecological, social and agricultural effects of cannabis production, but little is known about how growers produce this crop. Using an online survey, we gathered information from growers in July 2018 on their production practices. According to responses from about 100 growers, most cannabis was produced outdoors or in greenhouses, relied primarily on groundwater and used biologically based inputs for pest management. Many farms employed seasonal workers paid at fixed piece rates. Regulatory compliance varied according to farm size. Beginning to document growing practices will help scientists formulate key environmental, social and agronomic questions and develop relevant research and extension programs to promote best management practices and minimize negative environmental impacts of production.