Eelgrass (Zostera marina) is the most widely occurring marine angiosperm in the world and the primary type of subtidal vegetation found in estuarine ecosystems on the continental west coast. Eelgrass beds function as critical nurseries and spawning sites for a variety of invertebrates and fish, including the Dungeness crab, Pacific herring, and salmonids, and provide foraging habitat for many birds. Because of its important ecosystem functions, eelgrass is protected as Essential Fish Habitat by the National Marine Fisheries Services, providing it with regulatory protection. Impacts to this often under-appreciated resource are accounted for using pre- and post-construction monitoring. However, it can be challenging to tease apart project-related impacts from natural and climate- related fluctuations in eelgrass distribution and density, which can affect a project’s mitigation obligations. The establishment and long-term monitoring of reference sites can help these analyses and inform mitigation strategies. Here we present an overview of eelgrass survey methods, limitations of each method, and best practices for monitoring eelgrass beds in the face of elevated variability in marine ecosystems driven by climate change.