<p> Standardized sampling and genetic barcoding have transformed our ability to quantify the biodiversity of cryptic marine fauna. Most studies have focused on quantifying diversity in archetypically diverse marine habitats, such as tropical coral reefs. In this study, Autonomous Reef Monitoring Structures (ARMS), DNA barcoding, and morphology-based taxonomic identifications were utilized to characterize patterns of diversity within a large temperate estuary and inland sea in the NE Pacific Ocean. Globally, crustaceans constitute one third of all described marine species and were the focus of this study. ARMS were deployed at five sites across the southern Salish Sea (Strait of Juan de Fuca, San Juan Islands, and Puget Sound, Washington, USA). Forty-one species of crustacean were documented. Species diversity increased oceanward, highest in the northern sites closest to the entrance to the Pacific Ocean, mirroring diversity trends seen in other estuary systems. Overall patterns of crustacean diversity in the region were comparable to diversity estimates from ARMS in subtropical coral reefs or temperate oyster beds, underscoring the remarkable diversity of the northeastern Pacific invertebrate fauna.</p>