Historic and ongoing sediment contamination adversely affects estuaries, among the most productive marine ecosystems in the world. However, all estuaries are not the same, and estuarine sediments cannot be treated as either fresh or marine sediments or properly assessed without understanding both seasonal and spatial estuarine variability and processes, which are reviewed. Estuaries are physicochemically unique, primarily because of their variable salinity but also because of their strong gradients in other parameters, such as temperature, pH, dissolved oxygen, redox potential, and amount and composition of particles. Salinity (overlying and interstitial) varies spatially (laterally, vertically) and temporally and is the controlling factor for partitioning of contaminants between sediments and overlying or interstitial water. Salinity also controls the distribution and types of estuarine biota. Benthic infauna are affected by interstitial salinities that can be very different than overlying salinities, resulting in large-scale seasonal species shifts in salt wedge estuaries. There are fewer estuarine species than fresh or marine species (the paradox of brackish water). Chemical, toxicological, and community-level assessment techniques for estuarine sediment are reviewed and assessed, including chemistry (grain size effects, background enrichment, bioavailability, sediment quality values, interstitial water chemistry), biological surveys, and whole sediment toxicity testing (single-species tests, potential confounding factors, community level tests, laboratory-to-field comparisons). Based on this review, there is a clear need to tailor such assessment techniques specifically for estuarine environments. For instance, bioavailability models including equilibrium partitioning may have little applicability to estuarine sediments, appropriate reference comparisons are difficult in biological surveys, and there are too few full-gradient estuarine sediment toxicity tests available. Specific recommendations are made to address these and other issues.