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Located just east of Missoula, Montana, Milltown Dam stood from 1908 to 2008 immediately downstream of the Clark Fork River’s confluence with the Blackfoot River. After the discovery of arsenic-contaminated groundwater in the nearby community of Milltown, as well as extensive deposits of contaminated sediment in the dam’s upstream reservoir, in 1981, the area was designated a Superfund site – along with much of the Upper Clark Fork Watershed. This motivated the eventual decision to remove the dam, perform environmental remediation, and reconstruct approximately five kilometers of the Clark Fork River and its floodplain. This study is part conceptual and part empirical. It describes a state-and-transition framework equipped to investigate channel evolution as well as the adjustment trajectories of other socio-biophysical landscapes. This framework is then applied to understand the post-restoration channel evolution of the Clark Fork River’s mainstem, secondary channels, and floodplain. Adopting a state-and-transition framework to conceptualize landscape evolution lets environmental managers more effectively anticipate river response under multiple disturbence scenarios and therefore use more improvisational and adaptive management techniques that do not attempt to guide the landscape toward a single and permanent end state. State-and-transition models can also be used to highlight the spatially explicit patterns of complex biophysical response. The state-and-transition models developed for the Clark Fork River demonstrate the possibility of multiple evolutionary trajectories. Neither the secondary channels nor the main channel have responded in a linear, monotonic fashion, and future responses will be contingent upon hydrogeomorphic and climatic variability and chance disturbances. The biogeomorphic adjustments observed so far suggest divergent evolutionary trajectories and that in some instances the long-term fates of the mainstem, floodplain, and secondary channels are inescapably enmeshed with one another.

The hills of Yazoo Basin have a long history of land use modification and subsequent erosion and flood control issues. In response, federal actions were taken to address these issues beginning after the Mississippi River flood of 1927. Four major flood control reservoirs were built in 1932-1957, and instream low-drop grade control structures (GCS) were installed beginning in the 1980s. The objective of my dissertation was to ascertain the long-term effects of these efforts on stream fish assemblages and channel morphology. To assess whether the reservoirs affected upstream fish assemblages as barriers to recolonization by fluvial fishes or as source population for invasion by lentic generalist fishes (Chapter 1), I used stream data collected 43-61 years after the rivers were impounded to test for differences in fish assemblages between sites upstream and downstream of the reservoirs. Analysis of catch per effort and diversity metrics displayed little influence of the reservoirs, but trait-based analysis revealed marginal increases in planktivores, herbivores, detritivores, and generalists in upstream assemblages. After determining that potential effects of reservoirs would not confound further analysis, I assessed the effects of GCS on channel morphology (Chapter 2) and fish assemblages (Chapter 3) 30 years post-installation. To assess GCS effects on channel morphology, stream cross-sections were used to calculate Bank Height Ratio, Width/Depth Ratio, and Entrenchment Ratio, while point estimates made along the transects were used to calculate the average sediment size distribution. Analyses revealed that the GCS were successful in checking channel incision moving headward in the streams: sites upstream of the GCS were less incised and had greater accumulations of fine substrates compared to downstream sites and sites on streams lacking erosion control structures. The GCS could potentially affect fish assemblages through habitat modification or by selectively filtering the assemblages as a barrier to upstream migration. Analysis of beta diversity revealed that diversity was driven by species replacement rather than nestedness, which indicates GCS were not acting as filters on the assemblages. Analysis of catch per effort data confirmed differences in assemblage structure that echoed the instream habitat differences revealed in Chapter 2.

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