An understanding of the spatial and temporal diversity of benthic invertebrates is necessary to understand, manage, and protect freshwater habitats. Benthic invertebrates are important components of aquatic ecosystems and are frequently used in bioassessment and biomonitoring programs. Benthic invertebrates can also play a role in nutrient cycling in lentic environments through bioturbation activities. This dissertation uses a range of techniques and analyses to understand the arrangement of benthic invertebrate diversity in Upper Klamath Lake, Oregon, and several watersheds in northern southern California. Upper Klamath Lake (UKL) is a large, shallow, naturally eutrophic lake that has experienced declines in water quality, which has led to annual cyanobacterial blooms of Aphanizomenon flos-aquae. Benthic invertebrates can increase autochthonous nutrient cycling through benthic bioturbation activities. In order to better understand the role that benthic invertebrates play in UKL, I studied the density, taxonomic richness, and species composition of benthic invertebrate assemblages in three geographic regions (north, central, and south) and three habitats (littoral, open-water and trench) across UKL. I also characterized sediment composition and water quality at each collection site and determined which environmental variables correlated with differences in benthic invertebrate composition. This research is located in Chapters 1 and 3 of this dissertation. Like benthic invertebrates in UKL, the mayfly Baetis tricaudatus is an abundant and ecologically important organism of freshwater ecosystems. Despite its widespread distribution, B. tricaudatus cannot be consistently and accurately identified and belongs to a species group known to have cryptic species diversity. While previous studies have examined the spatial distribution of this diversity, none have studied the temporal distribution. To better understand the temporal arrangement of diversity at the cytochrome oxidase subunit 1 (CO1) mitochondrial gene region, I collected B. tricaudatus specimens from 3 sites over 4 years and used haplotype networks to visualize diversity. Because my results were different than those from other studies on the same taxon, for my final chapter I analyzed Baetis rhodani group COI sequences from northern and southern California using Bayesian phylogenetic analyses and haplotype networks. This research contributes to our understanding of genetic diversity, which is an important component to biodiversity.