Rivers have a fundamental importance to human civilization and are considered the primary source of renewable freshwater supply for societies worldwide. Human prosperity depends heavily on surface water and the groundwater it replenishes, but this growth often comes with a heavy cost to river health. Rivers worldwide and particularly in arid climates have experienced profound levels of human alterations, particularly through damming, that affect flow patterns, channel form, and species composition. Functional flows theory offers a promising method to characterize ecologically-important aspects of flow and how changes to flow patterns may affect ecosystems. The goal of this dissertation is to quantify and understand hydrologic alteration of rivers and its ecological effects using a functional flows approach. This work validates functional flows as an effective strategy for ecological streamflow analysis with evidence that they can be used to differentiate California’s natural flow regimes, quantify streamflow response to climate change, and reveal the links between flow management and riparian forest health. Chapter 1 describes creation of a novel tool to quantify functional flow metrics for Mediterranean streamflow patterns using time series analysis methods. Chapter 2 characterizes climate-caused changes to streamflow in snowmelt-dependent regions of California, highlighting the importance of both temperature increase on functional flow change and human emissions levels on potential outcomes. Chapter 3 describes an ecohydrologic field study linking riparian cottonwood growth to functional flows and offers promising evidence that environmental flows can lead to measurable improvement in riparian forest productivity. This dissertation advances river science through the creation and implementation of new tools that can be used to balance human and ecological needs of streamflow.

Freshwater cyanobacterial harmful algal blooms (FCHABs) are an increasing threat to drinking water worldwide. Climate change and environmental degradation exacerbate naturally eutrophic water bodies and widen the geographic area where FCHABs are likely to occur. The health effects of toxin-producing cyanobacteria are well-known, but their concentrations are unregulated in drinking water. So monitoring efforts are voluntary, which limits the data available for comprehensive analyses and hinders water utilities’ ability to prepare for and manage FCHABs events. FCHABs can cause human health, economic, and ecological damages, however, their socioeconomic impacts have not been quantified for vulnerable communities that are exposed seasonally to toxin-producing FCHABs in drinking water sources. This multidisciplinary study sheds light on four issues: (1) the risk of FCHAB development related to climate change; (2) the efficacy of current treatment solutions for public water supply; (3) drinking water affordability, especially for vulnerable communities; and (4) the lack of regulation and funding mechanisms for FCHABs. Five analyses were performed to evaluate the impacts of FCHAB management on drinking water sources. First, a risk analysis was developed to predict microcystin concentrations based on cumulative winter inflow. Second, the efficacy of surface water treatment plants in Lake County was evaluated to assess if public water systems (PWSs) adequately remove microcystin concentrations from finished drinking water supplies. Third, a water rate analysis for the surface water systems in Lake County assesses if there is a relationship between FCHABs and water rates. Fourth, water treatment chemical costs for four water systems in Lake County were calculated over a period of five years to assess if a relationship exists between water treatment cost and FCHAB events. Finally, a regulatory analysis assesses if the current regulatory proceedings lack an adequate funding mechanism for increases in the cost of water treatment due to FCHABs. The results of this study indicate that (1) FCHABs will continue to worsen with climate change; (2) surface water systems in Lake County adequately remove microcystins from finished drinking water; (3) FCHABs create a disproportionate financial burden on vulnerable communities; (4) there is a positive relationship between the cost of water treatment and FCHABs; and (5) current funding mechanisms are inadequate for the increased cost of water treatment from FCHABs. The discussion explores an avenue for policy intervention to assist public water systems treating for FCHABs.

The Rio Grande-Bravo (RGB) Basin, shared by the United States and Mexico, is a water-scarce basin shaped by climatic, topographic, and ecosystemic contrasts. As part of the natural flow regime, floods support habitat creation by resetting the channel, regulating water quality, and controlling invasive species. However, since 1870 the region has faced considerable socioeconomic growth, which has heavily altered the natural hydrology, resulting in drastic degradation of river health.This research analyzes natural and regulated flood events in the Southern branch of the RGB Basin from 1900 to 2010 at six control points. Flood timing was described with central metrics and measures of spread, which were also used to compare differences between natural and regulated floods. Flood magnitude and frequency were analyzed using flood frequency analysis and magnitude prediction of the 2-, 5-, and 10-year floods. To compare magnitude and frequency of natural and regulated floods, two indexes were developed. The main findings are: (1) natural flood timing reflects the climatic drivers of two main headwaters: flood events during the snowmelt season in the northern branch above the cities Presidio and Ojinaga, and during the monsoon and tropical storm season in the southern branch; (2) in the regulated regime, floods occur earlier in the year, most notably at the basin outlet; (3) natural median floods range from 720 m3/s at the headwaters to 2,250 m3/s at the basin outlet; (4) regulated median flood magnitudes decrease 70% in four stations, with larger floods occurring in stations located upstream the river outlet, opposite to natural hydrology; (5) the 10-year natural flood estimates range from 2,055 m3/s to 6,083 m3/s; (6) natural flood estimates show a pattern of dry and wet periods; and (7) frequency of large floods decrease at all stations, most noticeably after 1960. Changes in flood timing, magnitude, and frequency have significant implications for physical, biogeochemical, and biological ecosystem functions. The life stages of several species are timed with floods, like fish spawning and migration. Physical and biogeochemical functions triggered by predictable, large floods support habitat creation by regulating water quality, preventing channel narrowing, depositing nutrients in the floodplain, and clearing out invasive species, amongst many other functions. Water management alternatives to reproduce functional flows, especially floods, have already been proposed by several authors, showing it is possible to restore ecological functions and satisfy human water management goals.

Most large rivers in California and much of the world have dams impeding their flow. These dams provide important benefits to society but have negatively affected river ecosystems and the aquatic organisms that live in them by disrupting the natural patterns of movement of water and sediment. To mitigate some of these harmful effects, river managers often turn to physical habitat restoration and environmental flow manipulation. All dams have designed reservoir release operations and many rivers downstream of them have habitat restoration projects, but rarely do managers design these to work together to yield the best combined outcome. This study investigates the potential to modify flood risk management releases to better support downstream habitat enhancement projects designed to provide endangered salmonid rearing habitat. This goal is accomplished using an hourly reservoir operations model, a one-dimensional sediment transport model, and a two-dimensional steady flow model combined with habitat suitability analysis. Results show that lower magnitude, longer duration flood releases have the potential to increase provision of rearing habitat during fry and juvenile rearing periods while also reducing operations and maintenance costs for the constructed restoration projects and providing ancillary benefits to water supply. Furthermore, because of the changed river corridor and sediment regime, the results indicate that pre-dam flows would not be ideal for meeting current management objectives of providing rearing habitat below the dam, and that flows reconciled to the current physical, ecological, and operational contexts would be more appropriate.

River basins are unique dynamic systems that depend on their natural hydrologic variability and streamflow diversity to provide a wide range of ecosystem services. However, on a global scale, the fragmentation of river networks and the dampening of environmental variability are increasing by the unforeseen pressures of climate change and anthropogenic disturbances, including unsustainable water withdrawals, dam constructions, and land-use change. These disturbances can accumulate, pushing the system beyond a threshold, inducing a regime shift, and leading the system to an alternative state. But how much forcing a river basin can take until the system undergoes a regime shift and into an alternative state? And how to assess ecological resilience of a river basin from anthropogenic and climatic disturbances? A resilience approach seeks to explain these dynamics, including understanding the ecosystem organization and functional flow traits that are inherently bound to the system’s adaptive capacity to maintain critical functions and processes during changing environmental conditions. In this work, I propose a tractable framework to evaluate the ecological resilience of river basins by assessing three measurable resilience attributes: alternative regimes, thresholds, and adaptive capacity using the transboundary Rio Grande - Bravo basin as a case study. The broader impact of this work is to advance into the general endeavor of moving forward from the theoretical understanding of resilience into a more tangible and quantifiable measure to assess it. But most importantly is the strong potential that this framework has to support conservation efforts, ecosystem management and inform current policy of river basins to understand and incorporate the inherent dynamism of ecosystems into water management.