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Freshwater ecosystems are rapidly being altered due to shifting patterns of land use, urbanization, water diversions, water storage, water transportation, runoff, waste, fishing, invasive species, and climate change. As we continue to put more pressure on our freshwater resources, our understanding of ecological processes and the effects of various disturbances on aquatic ecosystems will need to be keener than it is today. Aquatic invertebrates are powerful tools for the biological assessment of changing aquatic habitats and can help guide us in restoration efforts and management decisions. My research looks at the benthic macroinvertebrate assemblages in Upper Klamath Lake (UKL), Oregon and the Russian River watershed in Northern California. More specifically, I research the spatial and temporal distribution of benthic macroinvertebrates, and their relationships to chosen environmental variables. UKL has become hypereutrophic over the past century due to watershed development and two fish species endemic to the lake are on the federal endangered species list. Poor water quality is one of the factors shown to have caused declines in the endangered fish species' populations and benthic macroinvertebrates have been shown to potentially contribute to this poor water quality. My research aims to describe the benthic macroinvertebrate assemblages that are found in the lake and how they are dispersed spatially to help advise policy makers in their attempts to improve water quality in the lake. My research also uses DNA barcoding to examine the temporal distribution of haplotypes of a common mayfly, Baetis tricaudatus. A better understanding of the temporal dynamics of the "barcoding gene" within this biologically important species group might improve the speed and accuracy of freshwater bioassesment, particularly that using genetics.  In addition, examining a number of population parameters, including genetic diversity, migration rate and effective population size will expand our understanding of how species resist various disturbances (e.g., water level, pollution, changes in community composition) and inform our management decisions. While genetic barcoding is a relatively new tool in aquatic bioassment applications, I believe it has tremendous potential to help guide us in understanding, and thus protecting, aquatic ecosystems.