With approximately 12,000 acres of marine habitat, San Diego Bay is the largest naturally occurring marine embayment between San Francisco and Scammon’s Lagoon (central Baja CA) and is home to a wide diversity of species (Allen et al. 2002). This important ecosystem is highly productive, with an abundance of juvenile fish supported by the extensive eelgrass nursery habitat. Nearby ecosystems are supported by production in San Diego Bay, as the fish migrate out into the open ocean once they have reached adulthood. Eelgrass is used as shelter for fish larvae settling in estuaries and by juvenile fish prior to migration from the brackish bay into the ocean (Jenkins and Wheatley 1997). Areas in which eelgrass have been growing in the bay were georeferenced using GIS files in Google Earth, and show measureable growth from 2004 to 2011, with the area increasing from 1561.5 acres in 2004 to 1871.1 acres in 2011. The Vantuna Research Group at Occidental College has conducted a biannual survey and complete sampling of the fish assemblages in 2005, 2008, and is midway through 2012 sampling. The purpose of this project was to assess the population and location of eelgrass-associated fish species in the bay using data collected throughout the seven-year time period. In past research it was found that measurements at eelgrass sites yielded nearly twice as many individual fish and fish species than samples taken at non-vegetated sites (Hoffman et al. 1986); therefore it was hypothesized that the increase in eelgrass should correlate to an increase in the abundance of eelgrass-associated fish assemblages. Species surveyed for this project were Syngnathus leptorhynchus, bay pipefish; Cymatogaster aggregata, shiner perch; Fundulus parvipinnis, California killifish; Heterostichus rostratus, giant kelpfish; and Leptocottus armatus, Pacific staghorn sculpin. Though much sampling has been done in years past, there had been no further investigation into precisely which areas of the bay these five fish species are found relative to the presence of eelgrass. A higher abundance of this assemblage was present in vegetated areas (defined as regions containing eelgrass) versus non-vegetated areas, and an increase in this assemblage was found over time. Standard lengths of the fish assemblage were also studied in order to note trends in vegetated versus non-vegetated area to show that smaller and presumably juvenile fish were more likely to be found in the vegetated areas of the bay. For the five species studied, there was a higher abundance of fish in the smaller size classes in the vegetated areas versus the non-vegetated areas. Exceptions to this pattern were noted and are likely due to generic habitat preferences and alternative reproductive cycles in individual species.