Thom, R.; Southard, S., and Borde, A., 2014. Climate-linked mechanisms driving spatial and temporal variations in eelgrass (Zostera marina L.) growth and assemblage structure in Pacific Northwest estuaries, USA.Using laboratory experiments on temperature and leaf metabolism, and field data sets from Washington, between 1991 and 2013, we developed lines of evidence showing that variations in water temperature, mean sea level, and desiccation stress appear to drive spatial and temporal variations in eelgrass (Zostera marina). Variations in the Oceanic Niño Index (ONI) and mean sea level (MSL), especially during the strong 1997–2001 El Niño-La Niña event, corresponded with variations in leaf growth rate of an intertidal population. Field studies suggested that this variation was associated with both desiccation period and temperature. Subtidal eelgrass shoot density recorded annually over a 10-year period was lowest during the warm and cool extremes of sea surface temperature. These periods corresponded to the extremes in the ONI. Variations in density of a very low intertidal population in a turbid estuary were explained by both variations in temperature and light reaching the plants during periods of higher MSL. These results show complex interactions between water-level variation, temperature and light as mechanisms regulating variation in eelgrass, which complicates the ability to predict the effects of climate variation and change on this important resource. Because of the extensive wide geographic distribution of eelgrass, its tractability for study, and its responsiveness to climate, this and other seagrass species should be considered useful indicators of the effects of climate variation and change on marine and estuarine ecosystems.