A project to deepen shipping and entrance channels in Charleston Harbor was conducted from 1999 to 2002. This generated approximately 22 million cubic yards of sediment for offshore disposal. Assessments of biological and physical conditions in the Charleston Ocean Dredged Material Disposal Site and surrounding areas were conducted prior to deepening (1993–94), and partway through the disposal period (2000). Results from the 2000 survey are presented and compared to the baseline survey. The study area was composed of the disposal zone and surrounding areas and divided into 20 one square mile strata. Within each stratum, benthic grab samples were collected from ten random sites for analysis of sediment composition and contaminants and macrobenthic assemblages. No contaminant levels were above effects range low levels. Results revealed that sediments in the western strata had significantly higher silt/clay content in the 2000 survey when compared to baseline sediments, while sediments east of the disposal zone were similar to baseline. Analyses were performed on a subset of the benthic data that compared baseline to 2000 conditions in western and eastern strata. The benthic communities in western strata were altered following disposal operations. The benthic community east of the disposal area was not different from baseline conditions. These alterations in the benthic community were attributed to changes in bottom habitat characteristics rather than pollution effects.