Around the world, oligotrophic lakes are changing. Once pristine shores are increasingly covered in dense mats of periphyton, known as filamentous algae blooms (FABs). Periphyton blooms occur in lakes' infrequently monitored littoral zones and thus are likely underreported and poorly understood. While some blooms have known causes, such as increased groundwater nutrient levels or an influx of invasive species, many FABs occur for unknown reasons. This dissertation examines the drivers contributing to periphytic FABs. In three chapters, Lake Tahoe, California-Nevada, USA, is selected as a case study because, unlike many lakes, Tahoe has a long history of periphyton monitoring. Overall, eulittoral, splash zone, periphyton at Lake Tahoe did not show a biomass increase from 1982 through 2019. Periphyton was measured consistently at 0.5 meters depth at multiple locations. Thus, as lake level changed over a range of 2.5 meters, monitoring recorded the biomass of either the diatom and green algae dominated community that inhabited the near-surface substrate, or the cyanobacteria dominated community that thrived at greater depths. Trend analysis showed that the stalked diatom and green algae communities did not show a statistically significant change in biomass over time. However, the cyanobacteria measurements showed a significant decline in biomass over time. The effects of temperature, lake surface elevation, bed-shear stress, mid-lake nutrients, days since the measured substrate was last exposed to air, and photosynthetically active radiation on periphyton biomass were evaluated using Bayesian modeling. The monitored and derived drivers of algae explained 32% of the variability in Lake Tahoe periphyton biomass. Temperature, nitrate, days since last exposed, and photosynthetically active radiation had significant correlations with periphyton biomass. The model could be improved by adding additional relevant data, such as more localized nutrient information. Looking toward the future, climate change model results were analyzed to project periphyton community and biomass shifts over time in Lake Tahoe. Local climate change conditions will affect many of the drivers of periphyton, including warmer lake temperatures, more nutrient inflows, and greater variability in lake levels. Combining the many changes, two potential outcomes are offered. In one scenario, diatoms continue to dominate the euphotic zone of periphyton, but biomass increases. In the other scenario, an increase in nutrients and temperature shifts the lake towards a green algae dominated euphotic zone. In both scenarios, cyanobacteria are likely to remain the dominant periphyton in the sublittoral zone. These findings suggest that in addition to periphyton drivers, periphyton biomass and community composition should be continually monitored to understand potential change. Despite the need for more ecohydrological information, few studies analyze groundwater and periphyton. Even fewer programs consistently monitor groundwater and periphyton together. Barriers to studying this transition zone area are created by underlying geology, intra-lake and cross-lake landscape processes, benthic biological systems, and data gaps. Trusted and new periphyton and groundwater monitoring methods are reviewed, and recommendations are proposed for integrating these methods. Using these combined methods and the combined knowledge of interdisciplinary experties, we can further hydrology and ecology. The chapters of this dissertation provide rationale and methodologies for increased understanding of FABs. Ideas for further future research are provided in the conclusion section. This dissertation has been formatted so that the chapters standalone as individual manuscripts. Each chapter has its abstract and references within the chapter.

Residence times of dissolved substances and sedimentation rates in tidal channels are affected by residual (tidally averaged) circulation patterns. One influence on these circulation patterns is the longitudinal density gradient. In most estuaries the longitudinal density gradient typically maintains a constant direction. However, a junction of tidal channels can create a local reversal (change in sign) of the density gradient. This can occur due to a difference in the phase of tidal currents in each channel. In San Francisco Bay, the phasing of the currents at the junction of Mare Island Strait and Carquinez Strait produces a local salinity minimum in Mare Island Strait. At the location of a local salinity minimum the longitudinal density gradient reverses direction. This paper presents four numerical models that were used to investigate the circulation caused by the salinity minimum: (1) A simple one-dimensional (1D) finite difference model demonstrates that a local salinity minimum is advected into Mare Island Strait from the junction with Carquinez Strait during flood tide. (2) A three-dimensional (3D) hydrodynamic finite element model is used to compute the tidally averaged circulation in a channel that contains a salinity minimum (a change in the sign of the longitudinal density gradient) and compares that to a channel that contains a longitudinal density gradient in a constant direction. The tidally averaged circulation produced by the salinity minimum is characterized by converging flow at the bed and diverging flow at the surface, whereas the circulation produced by the constant direction gradient is characterized by converging flow at the bed and downstream surface currents. These velocity fields are used to drive both a particle tracking and a sediment transport model. (3) A particle tracking model demonstrates a 30 percent increase in the residence time of neutrally buoyant particles transported through the salinity minimum, as compared to transport through a constant direction density gradient. (4) A sediment transport model demonstrates increased deposition at the near-bed null point of the salinity minimum, as compared to the constant direction gradient null point. These results are corroborated by historically noted large sedimentation rates and a local maximum of selenium accumulation in clams at the null point in Mare Island Strait.

The UC Davis research involved a 24-month study (including a 4-month measurement program) in the Salton Sea to directly measure sediment resuspension using an array of OBS instruments and an acoustic wave height and current profiling instrument (AWAC). The data provided by these instruments, in conjunction with existing UC Davis temperature recording instruments in the Sea and the existing CIMIS meteorological network, point to the existence of a quasi-equilibrium condition for the suspension of sediments in the lake.

Non-linear relations were developed between the wind intensity and turbidity near which were in relative agreement with relationships from reviewed literature. In particular, the extended García and Parker formulation with DLM-WQ shows the best prediction to describe the seasonal trends as well as short-term variations. The relationship was incorporated into the existing DLM-WQ model.

DLM-WQ, combined with this new sediment model, was used to more fully explore the potential for ecological restoration of the Salton Sea under possible future configurations. Two scenarios, the North Sea Combined Alternative and South Sea Combined Alternative, as suggested by PEIR were examined. The simulation of North Sea Combined Alternative indicates that the Marine Sea might have a better eutrophic status than that of the whole Sea because of fewer sediment resuspension events due to lower average wind speed acting on a smaller surface. On the other hand, the simulation of South Sea Combined Alternative suggested that the concentrations of nutrients in the water column would be the same or higher than those of the whole Sea, because of more sediment resuspension events due to higher average wind speed and due to shallower water depth. In the both alternatives, however, the anoxia in the hypolimnion would be spatially and temporally increased due to increased stratification periods, during which time toxic substances (such as hydrogen sulfide) and organic materials could be accumulated in the sediments.

DLM-WQ with the new sediment algorithm successfully accounts for the dominant processes that control eutrophication in the current Salton Sea and provides an indication of variations in properties that could be expected in potential future configurations. In addition to being a tool for comparing future configurations, DLM-WQ provides a basis for designing future monitoring needs.