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Uncertainties in sediment quality assessments are discussed in five categories: (1) sediment sampling, transport and storage; (2) sediment chemistry; (3) ecotoxicology; (4) benthic community structure; and (5) data uncertainties and QA/QC. Three major exposure routes are considered: whole sediments, and waters in sediment pores and at the sediment-water interface. If these uncertainties are not recognized and addressed in the assessment process, then erroneous conclusions may result. Recommendations are provided for addressing the identified uncertainties in each of the key areas. The purpose of this paper is to improve the reporting of sediment quality assessments.