The St. Lucie estuary (SLE) ecosystem in South Florida has been shown to be contaminated with metals and pesticides. Our earlier studies also showed that aquatic organisms, especially benthic species in the SLE ecosystem, might be potentially at high risk from copper (Cu) exposure. The objectives of this study were to conduct studies with separate groups of organisms exposed to seven field-collected sediment samples from the St. Lucie River according to standard procedures to evaluate toxicity and tissue concentrations of Cu and zinc (Zn). Short term and longer term whole sediment acute toxicity studies were performed with Ampelisca abdita and Mercenaria mercenaria. Analysis of sediment chemical characteristics showed that Cu and Zn are of most concern because their concentrations in 86 % of the sediments were higher than the threshold effect concentrations for Florida sediment quality criteria and the National Oceanic and Atmospheric Administration Screening Quick Reference Tables (SQuiRTs) sediment values. There was no significant effect on survival of the tested organisms. However, increased Cu and Zn concentrations in the test organisms were found. Dry weight of the tested organisms was also inversely related to Cu and Zn concentrations in sediments and organisms. The effects on organism weight and Cu and Zn uptake raise concerns about the organism population dynamics of the ecosystem because benthic organisms are primary food sources in the SLE system and are continuously exposed to Cu- and Zn-contaminated sediments throughout their life cycle. The results of the present study also indicate that Cu and Zn exposures by way of sediment ingestion are important routes of exposure.