Freshwater ecosystems support biodiversity, climate resilience, and ecosystem services around the globe, making them a conservation priority. To effectively conserve diverse freshwater ecosystems in an uncertain climate future, we must employ a portfolio of conservation strategies that tackle complementary aspects of freshwater restoration and conservation. This dissertation explores three conservation strategies - area-based conservation, local restoration, and wildlife reintroduction - as approaches to conserving freshwater ecosystems. Chapter one examines how state or national area-based conservation schemes must shift focus to specifically include freshwater ecosystems, providing climate, biodiversity, and societal benefits while also better protecting freshwater systems. Our recommendations for centering freshwater ecosystems are to 1) focus on watershed-scale conservation; and 2) consider five freshwater ecosystem priorities, including connectivity, watershed disturbance, flow alteration, water quality, and biodiversity. Chapter two zooms in to a local restoration project in the Klamath River watershed in northern California, where hydropower development and high river water temperatures threaten juvenile salmonids. We show that human-made off-channel floodplain ponds provide cooler and more stable thermal refuge habitat for salmonids, illustrating the value of small-scale restoration in systems that are highly impacted by human development. Chapter three takes a different perspective on habitat engineering by exploring how reintroducing a native wildlife species, the North American beaver (Castor canadensis), could have both biodiversity and climate resilience (water storage and fire risk) benefits at the landscape scale. Our results show that after centuries of overutilization, considerable capacity for beaver dams remains throughout the California Sierra Nevada region. We also show that beavers have the potential to store significant surface water and create fire resilient landscapes throughout the region, illustrating how restoring a keystone species can benefit both ecosystems and society. Overall, these chapters represent three valuable and intersecting approaches to conserving and restoring resilient and functional freshwater ecosystems.