Seagrasses are critically important components of many marine coastal and estuarine ecosystems, but are declining worldwide. Spatial change in distribution of eelgrass, Zostera marina L., was assessed at Bahía San Quintín, Baja California, Mexico, using a map to map comparison of data interpreted from a 1987 Satellite Pour l'Observation de la Terre multispectral satellite image and a 2000 Landsat Enhanced Thematic Mapping image. Eelgrass comprised 49% and 43% of the areal extent of the bay in 1987 and 2000, respectively. Spatial extent of eelgrass was 13% less (-321 ha) in 2000 than in 1987 with most losses occurring in subtidal areas. Over the 13-yr study period, there was a 34% loss of submerged eelgrass (-457 ha) and a 13% (+136 ha) gain of intertidal eelgrass. Within the two types of intertidal eelgrass, the patchy cover class (<85% cover) expanded (+250 ha) and continuous cover class (≥85% cover) declined (-114 ha). Most eelgrass losses were likely the result of sediment loading and turbidity caused by a single flooding event in winter of 1992-1993. Recent large-scale agricultural development of adjacent uplands may have exacerbated the effects of the flood. Oyster farming was not associated with any detectable losses in eelgrass spatial extent, despite the increase in number of oyster racks from 57 to 484 over the study period.