Recent advances in remote-sensing technologies and analysis methods, specifically airborne-LiDAR elevation data and corresponding geographical information system (GIS) tools, present new opportunities for automated and rapid fluvial geomorphic (FGM) assessments that can cover entire watersheds. In this thesis, semi-automated GIS tools are used to extract channel centerlines and bankfull width values from digital elevation models (DEM) for five New England watersheds. For each study site, four centerlines are mapped. LiDAR and NED lines are delineated using ArcGIS spatial analyst tools with high-resolution (1-m to 2-m) LiDAR DEMs or USGS National Elevation Dataset (NED) DEMs, respectively. Resampled LiDAR decreases LiDAR DEM resolution and then runs spatial analyst tools. National Hydrography Dataset (NHD) lines are mapped by the USGS. All mapped lines are compared to centerlines delineated from photography and LiDAR DEMs. Bankfull widths at each site are determined through three methods. Regional regression equations are applied using variables derived from LiDAR and NED DEMs separately, producing two sets of width results. Additionally, the Hydrogeomorphological Geoprocessing Toolset (HGM) is used to extract widths from LiDAR data. Widths are also estimated visually from aerial photos and LiDAR DEMs. Widths measured directly in the field or derived from field-data are used as a baseline for comparison. I find that with a minimal amount of preprocessing, specifically through DEM resampling, LiDAR data can be used to model a channel that is highly correlated with the shape and location of the mapped channel. NED-derived channels model the mapped channel shape with even greater accuracy, and model the channel location only minimally less accurately. No tool used in this study accurately extracted bankfull width values, but analysis of LiDAR data by the HGM toolset did capture details that could not be resolved using regression equations. Overall, I conclude that automated, computerized LiDAR interpretation needs to improve significantly for the expense of data collection to be cost-effective at a watershed scale.

Environmental perturbations are ubiquitous features of ecosystems and shape ecological structure and function. Climate change will alter the intensity and frequency of disturbances and expose ecosystems to novel combinations of useful inputs (subsidies) and harmful inputs (stressors). Coastal wetlands are particularly vulnerable to changing environmental conditions and are increasingly exposed to effects of interacting subsidies and stressors. In particular, the Florida Coastal Everglades, which has experienced accelerated change due to a history of water management practices, is vulnerable to new disturbances associated with climate change. The low-lying Florida Everglades faces multiple disturbances from storm surge, nutrient enrichment, and sea-level rise which will influence its responses to future environmental perturbations. Microbial communities are often used to characterize environmental change because of their high surface area to volume ratio, permeable membrane, and quick turnover rates. Therefore, assessing how microbial function changes can provide insights into how subsidies and stressors interact to alter biogeochemical cycles. I tested how nutrient enrichment can alter ecosystem responses to stress and found that it did not promote recovery in mangrove plants. I examined how long-term exposure to salinity and phosphorus (the limiting nutrient in the Everglades) affected microbial enzyme activity and found that salinity alone acts as a suppressor of enzyme activity but phosphorus addition can mitigate salinity stress in sawgrass soil. I tested how pulses of salinity can affect the microbially-mediated breakdown of organic material and found that the microbial community was functionally redundant and unaffected by saltwater pulses; however, microbial activity was consistently lower in the brackish marsh compared to the freshwater marsh. I investigated how gradients of salinity and phosphorus affected freshwater and brackish soils and determined previous exposure to saltwater intrusion dominates affects microbial function and soil composition. Across these experiments, I found that environmental perturbations alter the microbial-mediated processing of nutrients and carbon, and legacies of previous disturbances influence the microbial response to new disturbance regimes.

There is a need to define a more efficient and accurate approach to aquatic habitat mapping. Traditional approaches have focused on intense biological/non-biological sampling and observation analysis within specific and restrained scales. Therefore, an underwater video mapping system (UVMS) has been developed in efforts to identify federally protected aquatic species’ habitats within the Obed Wild and Scenic River (OBRI). The UVMS kayak apparatus provides georeferenced video footage correlated with GPS (global positioning systems) for GIS (geographic information systems) mapping applications. Based on its fluvial and geomorphological trends, OBRI was dissected quantitatively and integrated into databases for species-specific GIS habitat queries. Substrate type, depth, above water river characteristics (pool/riffle/run), and substrate embeddedness were extracted to access specific habitats. To better pinpoint optimal microhabitat locations, a physical habitat suitability model was developed to rank preferred habitat locales. Rankings were sequentially broken into five categories: optimal, sub-optimal, marginal, sub-marginal, and poor habitat criteria. Habitat suitability findings for the interested species habitats varied tremendously, favoring fish species. Spotfin chub, Erimonax monacha, optimal habitat was found to cover 22.14 km of river length within OBRI (30 % of OBRI’s spatial extent). The blackside dace, Phoxinus cumberlandensis, (38.9 km) and the duskytail darter, Etheostoma percnurum, (50.9 km) met optimal habitat conditions that yielded 51% and 69% of OBRI’s spatial extent, respectively. In general, optimal habitats for the six mussels were sporadically distributed and had low occurrences. Primarily, these mussel species prefer highly embedded areas with very specific depths and pool/riffle/run conditions. Cumberland elktoe, Alasmidonta atropurea, optimal habitat ranges spanned across 4.32 km (6% of OBRI’s spatial extent) with most of the habitat characteristics in OBRI being marginal. The purple bean, Villosa perpurpurea, optimal habitat was identified within 2.61 km of OBRI (3.5% of OBRI’s spatial extent). Most of the physical conditions of OBRI supplied poor to sub-marginal habitat for the purple bean, at least from a thalweg perspective. Only 385 m coincided with optimal habitat for the cumberland bean, Villosa trabalis, (0.5% of OBRI’s spatial extent) with most habitats in long sub-marginal reaches. Optimal habitats for the cumberlandian combshell, Epioblasma brevidens, the tan riffleshell, Epioblasma florentina walkeri, and the littlewing pearlymussel, Pegias fibula, were deficient, only occurring in 484 m, 276 m, and 252 m of OBRI, respectively (0.7%, 0.4%, and 0.3% of OBRI’s spatial extent). Marginal to sub-marginal habitats dominated the park for these three mussel species.

Nutrient limitation in aquatic ecosystems results from a deficiency in nitrogen or phosphorus levels relative to cellular growth needs. Nutrient limitation of freshwater systems is a function of biotic and abiotic factors. Biotic factors include vascular and nonvascular plant community composition. Abiotic factors include underlying bedrock and land-use activities (e.g. agriculture, septic systems). Nutrient availability directly affects growth, productivity, and community structure of primary producers. The purpose of this study was two-fold: (1) to assess the relationship between ambient algal biomass. and in-stream nutrient levels along the longitudinal course of a river through a transition from weak to well-developed underlying karst bedrock, and (2) experimentally assess if periphyton was nitrogen or phosphorous limited between weak and well-developed karst sites. Sestonic and filamentous biomass (= chlorophyll-a) levels increased monthly along the longitudinal gradient. In contrast, periphyton biomass levels increased minimally monthly and displayed no longitudinal pattern. Nitrate and soluble reactive phosphorus levels exhibited distinct longitudinal increases, whereas total phosphorous displayed minimal change and ammonia levels decreased in the downstream direction. Total nitrogen (TN) levels increased upstream but decreased sharply in the well-developed downstream karst sites. The nutrient limitation assays revealed that the highest periphyton levels were with N + P treatments at the most upstream sites. Overall, in Kentucky's Green River algal biomass accrual appears to be mainly P-limited but likely also by TN availability during late summer.

There is a need to define a more efficient and accurate approach to aquatic habitat mapping. Traditional approaches have focused on intense biological/non-biological sampling and observation analysis within specific and restrained scales. Therefore, an underwater video mapping system (UVMS) has been developed in efforts to identify federally protected aquatic species’ habitats within the Obed Wild and Scenic River (OBRI). The UVMS kayak apparatus provides georeferenced video footage correlated with GPS (global positioning systems) for GIS (geographic information systems) mapping applications. Based on its fluvial and geomorphological trends, OBRI was dissected quantitatively and integrated into databases for species-specific GIS habitat queries. Substrate type, depth, above water river characteristics (pool/riffle/run), and substrate embeddedness were extracted to access specific habitats. To better pinpoint optimal microhabitat locations, a physical habitat suitability model was developed to rank preferred habitat locales. Rankings were sequentially broken into five categories: optimal, sub-optimal, marginal, sub-marginal, and poor habitat criteria. Habitat suitability findings for the interested species habitats varied tremendously, favoring fish species. Spotfin chub, Erimonax monacha, optimal habitat was found to cover 22.14 km of river length within OBRI (30 % of OBRI’s spatial extent). The blackside dace, Phoxinus cumberlandensis, (38.9 km) and the duskytail darter, Etheostoma percnurum, (50.9 km) met optimal habitat conditions that yielded 51% and 69% of OBRI’s spatial extent, respectively. In general, optimal habitats for the six mussels were sporadically distributed and had low occurrences. Primarily, these mussel species prefer highly embedded areas with very specific depths and pool/riffle/run conditions. Cumberland elktoe, Alasmidonta atropurea, optimal habitat ranges spanned across 4.32 km (6% of OBRI’s spatial extent) with most of the habitat characteristics in OBRI being marginal. The purple bean, Villosa perpurpurea, optimal habitat was identified within 2.61 km of OBRI (3.5% of OBRI’s spatial extent). Most of the physical conditions of OBRI supplied poor to sub-marginal habitat for the purple bean, at least from a thalweg perspective. Only 385 m coincided with optimal habitat for the cumberland bean, Villosa trabalis, (0.5% of OBRI’s spatial extent) with most habitats in long sub-marginal reaches. Optimal habitats for the cumberlandian combshell, Epioblasma brevidens, the tan riffleshell, Epioblasma florentina walkeri, and the littlewing pearlymussel, Pegias fibula, were deficient, only occurring in 484 m, 276 m, and 252 m of OBRI, respectively (0.7%, 0.4%, and 0.3% of OBRI’s spatial extent). Marginal to sub-marginal habitats dominated the park for these three mussel species.

Semi-distributed hydrological models are often used for streamflow forecasting, hydrological climate change impact assessments, and other applications. In such models, basins are broken up into hydrologic response units (HRUs), which are assumed to have a relatively homogenous response to precipitation. HRUs are delineated in a variety of ways, and the procedure used may impact model performance. HRU delineation procedures have been researched, but it is still not clear how important these subdivision schemes are or which delineation methods are most effective. To start addressing this knowledge gap, this project investigated whether or not HRU size has a significant effect on streamflow simulation at the mouth of a watershed. To test this, 30 gaged, relatively unimpaired western U.S. basins were each modeled with 6 HRU sets of different sizes using the Precipitation Runoff Modeling System (PRMS). To isolate size as a variable, HRUs were delineated using stream catchments. For each basin, streams were defined with 6 different threshold levels, producing HRUs of differing sizes. Nineteen model parameters were derived for each HRU using nationally consistent GIS datasets, and all other model parameters were left at default values. Climate inputs were derived from a national 4-km2 gridded daily climate dataset. After calibration, 4 goodness-of-fit metrics were calculated for daily streamflow for each HRU set. Uncalibrated model performance was generally poor for a variety of reasons, but comparison of the models was still informative. Results for the 30 basins across the 6 HRU size classes showed that HRU size did not significantly impact model performance across all basins. However, in basins that had less total precipitation and higher elevation, sensitivity of model performance to HRU subdivision levels was slightly greater, though not significantly so. Findings indicate that, in most basins, little subdivision may be required for good model performance, allowing for desirable simplicity and fewer degrees of freedom without sacrificing runoff simulation accuracy.

The North Florence Dunal Aquifer is the only feasible source for drinking water for the coastal city of Florence, Oregon and Florence's Urban Growth Boundary. High infiltration rates and a shallow groundwater table leave the aquifer highly susceptible to contamination from septic tank effluent, storm runoff, chemical fertilizers and recreational ATV use throughout the dunes. Public interest in the quality and quantity of the aquifer water has been sparked since the City of Florence received a grant from the Environmental Protection Agency for a watershed protection and restoration project. Delineation of the shallow groundwater surface and its relationship to the surface water bodies within the dunes is crucial in protecting this drinking water source from contamination. This thesis project created a GIS representation of the shallow groundwater elevation and associated prediction error map. Surface water bodies were confirmed as window lakes into the dunal aquifer and no signs of perched aquifer conditions were observed between Holocene and Pleistocene dunes. Ground Penetrating Radar, well data provided by the city of Florence and LiDAR were the primary sources for data collection.

This study assessed the influence of landscape development on stream-associated amphibians in forested riparian areas within the Portland-Vancouver metropolitan region. Human alteration of landscapes may dramatically affect the ecology of neighboring aquatic systems. It was hypothesized that lotic amphibians would be negatively associated with greater amounts of landscape development and positively associated with forested area within the surrounding watershed. Thirty-seven 1st-3rd order streams were sampled between June 21st and September 21st in 2011. Streams potentially providing adequate habitat for stream-obligate amphibians were randomly selected. Amphibians were surveyed along 30-meter stream transects using an active-cover search (ACS). Environmental variables associated with development in surrounding landscapes were measured in situ. GIS delineation was conducted to define landscape-scale variables at stratified distances from riparian networks up-stream of each site via the utilization of the 2006 NLCD dataset and a finer-scale, regional dataset compiled by the Institute for Natural Resources (INR). Amphibians were detected at seventeen of the thirty-seven sampled streams. The most commonly detected species were Dicamptadon tenebrosus, Plethadon vehiculum and Plethadon dunni. Streams where amphibians were observed had lower average water temperature and conductivity, coarser stream substrate and were located on public property more often than streams where no amphibians were detected. Landscape variables were most significant to amphibians within 100 and 200 meters of the upstream stream network. Occupancy of a site by facultative species was best explained by the proportion of mixed forest in the surrounding watershed (R2=0.343, p<0.001). Occupancy of a stream by obligate species was best predicted by measurements of water quality and in-stream cover (Water Temperature: R2=0.275, p<0.001; Water Conductivity: R2=0.248, p<0.001; Cover: R2=0.323, p<0.001). Occupancy of stream refugia by all observed amphibians was positively influenced by higher percentages of forest cover and lower percentages of urban development and herbaceous vegetation in the surrounding watershed. Results of this study indicate that urban refugia must contain adequate riparian forest area, coarse stream substrate and clean, cool water to sustain stream-amphibian communities. Protection of remnant forested headwater stream networks is essential to the conservation of lotic amphibians in this urbanized region.

Hydro-climate extreme analysis helps understanding the process of spatio-temporal variation of extreme events due to climate change, and it is an important aspect in designing hydrological structures, forecasting floods and an effective decision making in the field of water resources design and management. The study evaluates extreme precipitation events over the Columbia River Basin (CRB), the fourth largest basin in the U.S., by simulating four CMIP5 global climate models (GCMs) for the historical period (1970-1999) and future period (2041-2070) under RCP85 GHG scenario. We estimated the intensity of extreme and average precipitation for both winter (DJF) and summer (JJA) seasons by using the GEV distribution and multi-model ensemble average over the domain of the Columbia River Basin. The four CMIP5 models performed very well at simulating precipitation extremes in the winter season. The CMIP5 climate models showed heterogeneous spatial pattern of summer extreme precipitation over the CRB for the future period. It was noticed that multi-model ensemble mean outperformed compared to the individual performance of climate models for both seasons. We have found that the multi-model ensemble shows a consistent and significant increase in the extreme precipitation events in the west of the Cascades Range, Coastal Ranges of Oregon and Washington State, the Canadian portion of the basin and over the Rocky Mountains. However, the mean precipitation is projected to decrease in both winter and summer seasons in the future period. The Columbia River is dominated by the glacial snowmelt, so the increase in the intensity of extreme precipitation and decrease in mean precipitation in the future period, as simulated by four CMIP5 models, is expected to aggravate the earlier snowmelt and contribute to the flooding in the low lying areas especially in the west of the Cascades Range. In addition, the climate change shift could have serious implications on transboundary water issues in between the United States and Canada. Therefore, adaptation strategies should be devised to cope the possible adverse effects of the changing the future climate so that it could have minimal influence on hydrology, agriculture, aquatic species, hydro-power generation, human health and other water related infrastructure.

Methyl halides are trace gases with both natural and anthropogenic origins. Once generated, these gases transport chlorine and bromine into the stratosphere, where they play an important role in ozone depleting catalytic cycles. The Florida Everglades is one location where methyl halide emissions have been proposed to be elevated due to high primary production and ionic halogens. This region also provides a unique study environment due to salt water intrusions, which occur during storm or low marsh water level-high tide events. The purpose of this research was twofold. First, quantification of methyl chloride (CH3Cl) and methyl bromide (CH3Br) production from periphyton mats on a temporal scale was needed. Secondly, to determine how varying concentrations of salinity affect CH3Cl and CH3Br production originating from calcareous periphyton mats within the Everglades. Periphyton was exposed to continuous 12 hour dark/light cycles in varying concentrations of salt water (0, 0.1, 1, 5, and 10 parts per thousand). All water samples were analyzed to determine the production rate of CH3Cl and CH3Br in periphyton samples using a gas chromatograph coupled with an electron capture detector (GC-ECD). Periphyton mats were found to be a producer of CH3Cl in all freshwater (0 parts per thousand) trials and sampling times; however, results from CH3Br analysis found production rates that suggest consumption occurred in the majority of the 0 parts per thousand trials. Production rates for CH3Cl ranged from 0.077 to 0.109 g-1hr-1 after 24 hours, 0.027 to 0.073 pM g-1hr-1 after 48 hours, and 0.034 to 0.047 pM g-1hr-1 after 72 hours. Production rates for the CH3Br freshwater experiments ranged from -0.00025 to 0.00185 pM g-1hr-1 after 24 hours, -0.00022 to -0.00078 pM g-1hr-1 after 48 hours, and -0.00042 to -0.00061 pM g-1hr-1 after 72 hours. This research has also shown that increased salinity does have a significant positive effect on the production of CH3Cl and CH3Br from calcareous periphyton mats, which is important in areas that could be prone to salt water intrusions or rising sea levels due to global climate change.