We present a quantitative study of the effects of sea surface temperatures on eelgrass productivity variables. We compared standing stock variables for Zostera marina for the strong El Niño event of 1986–1987, previously published by other workers for San Quintín Bay, Baja California, to our previously unpublished data for the “normal year” of 1992–1993. We found significant differences for most of the variables measured, which included Leaf Area Index, leaf length, width, dry weight and area, biomass, shoot density, and number of leaves per shoot. Inspection of the multivariate ENSO index (MEI) and sea surface temperature (SST) anomalies for each of these years showed that the differences could be explained by the warm SSTs associated with the ENSO event. We were able to explain the observed differences from a dynamic perspective by using a leaf-growth model forced by SSTs. We conclude that sea surface temperature summarizes the fundamental environmental influences on eelgrass leaf dynamics observed in our study site. That is, higher SSTs explain the reduction in mean leaf lengths and the corresponding diminution in related productivity variables. This study also strengthens the view that the onset of an El Niño event provides anticipatory evidence for the effects that a rise in global temperature is expected to elicit in eelgrass beds.