In mountainous terrain, road-crossings may impair creeks by impeding fish passage, increasing sediment delivery to stream channels, and altering surface and subsurface flow paths. The objectives of this study were to quantify the short-term impacts of 6 road-crossing reconstruction projects on alluvial creeks in the Klamath National Forest of California. I used a Before-After-Control-Impact study design with 1 set of data pre-construction, 1 set of data immediately following construction, and 2 sets of data over the following 2 yr. The data included measures of fine-sediment deposition, grain-size, longitudinal-profiles, cross-sections, and benthic macroinvertebrates. This study found little impact on fine-sediment deposition or grainsize. The majority of longitudinal-profiles and cross-sections tended to incise upstream in response to culvert replacement, but the responses were largely site-specific. Furthermore, most morphological changes in slope and bed elevation were minimal. Most of the commonly used biological metrics did not show significant changes, but I observed significant changes (P = 0.005) in the populations of 3 orders of insects (Ephemeroptera, Plecoptera and Trichoptera) that are often used as indicators of disturbance and are a primary salmonid food source. This study upholds Best Management Practices as an effective technique for salmonid habitat restoration.

Human disturbance at global and local scales is profoundly impacting stream ecosystems in California. For example, climate change, which is considered a form of human disturbance in this dissertation, is causing notable increases in air temperature and decreases in precipitation in some regions of the state. These changes are outside the range of natural variability and are expected to intensify. Furthermore, these changes affect stream-water temperatures, stream-flow levels, and aquatic biota. Human disturbance at the local scale in California includes, but is not limited to, urbanization, the development and use of land for timber extraction and agriculture, and manipulation of habitats for recreation or for the preservation of endangered species.

I examined the impacts of global change and human disturbance on stream ecosystems in Northern California at a variety of sites and using a variety of biological and physical techniques. The sites were located in five California counties, including Lake, Marin, Napa, Siskiyou, and Sonoma. Monitoring and analytical techniques for benthic macroinvertebrates used both standard and novel approaches and metrics of biological assessment. Physical techniques included surveys of channel widths and longitudinal profiles, bankfull-channel estimates, flow measurements, pebble counts, fine-sediment measurements, and large-wood inventories, which were analyzed using a variety of geomorphological and hydrological approaches.

I found that: 1) the common metrics used in biological assessment will have continued applicability for biological assessment programs in Northern California and that a new metric for detecting climate-change effects could be developed; 2) stream-crossing reconstruction was causing increased patchiness of benthic-macroinvertebrate communities in the short term; 3) vineyard water-withdrawals were having an effect on stream communities that occurred after a threshold level of vineyard coverage and extent was reached; and 4) the addition of engineered, large-wood structures to streams for physical-habitat restoration increased pool frequency and caused changes in the benthic community, although the resulting levels of large wood in the channels were still lower than levels typically found in other regions of the northwestern United States.

Many dams built over the last century in California no longer provide their intended benefits and may pose ecological and safety risks. However, a lack of clear regulatory framework, further complicated by a lack of scientific understanding of the impacts of dam removal, has handicapped many efforts to remove such outmoded dams. We investigate these challenges through a case study of York Creek Dam in St. Helena, California and show the need for standard protocols to prioritize and monitor dam removals. As a thought experiment, we explore how dam removal would proceed under the European Union Water Framework Directive (WFD) and argue that California can learn from the WFD’s systematic, watershed approach to improve dam removal decision-making. However, the monitoring programs under the WFD are driven by ecology and therefore provide little guidance on monitoring channel changes to evaluate whether dam removal increases the risk of flooding for downstream property, a major concern in California.