A portable seismic array was deployed in the San Diego area at a suite of geologic sites in order to investigate local site effects on weak ground motion. A total of 161 events from both local and near-regional earthquakes were recorded and used in the analysis. Recording sites included stations underlain by Holocene-age fill, alluvium, bay sediments and artificial fill, Quaternary-age and Tertiary-age formational deposits, and crystalline rock exhibiting various degrees of weathering. The effects of local site conditions were evaluated using a least squares matrix factorization (LSMF) inversion algorithm to analyze horizontal S-wave arrivals. Site response amplitudes were determined for each station and each frequency from 1-20 Hz. The inversion method was used to separate the site effects from the combined effects of the source and path. In addition, several events from different azimuths were averaged to further reduce differential path effects. Spectral ratios of S-wave coda were also used to estimate site response at two of the study sites. The coda analysis results were generally consistent with the results obtained from the inversion analysis. Site response amplifications up to 15 times that of a crystalline rock reference site, R4, were observed at a site underlain by artificial fill and bay sediments, S1. An additional site underlain by bay sediments, S2 exhibited a site response considerably different from the S1 site. Ground motion amplifications were nearly 75 percent less at the S2 site than the S1 site and were found to be more consistent with the site response observed at sites underlain by more indurated deposits. The site response observed at the Quaternary- and Tertiary-age formational sites was fairly consistent with the response of the younger alluvial sites, which may be attributable to the relatively shallow burial of the formational deposits in San Diego. Site effects at one of the alluvial sites, S3, show evidence of varying over the time period of this study. A reduction in site response on the order of 4-5 times was observed at this site following the inundation of the site. This observation suggests that the subsurface conditions controlling site response were altered in such a way that the impedance in the near-surface layers was significantly changed, reducing the observed site response. The site response at the five crystalline rock sites included in the study were consistent at frequencies below 4 Hz, but become more distinct with an increase in frequency. Based on seismic P-wave refraction data collected at the crystalline rock sites, this deviation in response at higher frequencies appears to be directly related to the presence of weathered horizons in the near-surface at these sites. Amplifications on the order of 6 times that of a slightly weathered crystalline rock reference site, R4, were observed at a study site underlain by highly weathered crystalline rock.