Sediments represent an important repository of pollutants and a source of contamination for the aquatic food web. Toxicity tests using amphipods as test-organisms have been employed in the assessment of marine and estuarine sediments, together with chemical analyses. The present work aimed to evaluate the quality of sediments from six stations situated in the Santos and São Vicente Estuarine and Harbour System (São Paulo - Brazil) using acute whole sediment toxicity tests with amphipods (Tiburonella viscana) and chemical analyses of metals, PCB's, and PAH's. Other sediment parameters, such as organic carbon and grain size distribution were also analysed. Higher contamination levels were observed in the internal portion of the estuary, where Santos harbour and the industrial zone are located. The toxicity tests showed significant adverse results for most of the samples tested, and the sediments from the internal portion of the estuary presented the highest toxicity. The principal component analyses (PCA) indicated a close relationship between sediment contamination and toxicity. Positive correlation of these factors in the samples studied was used to establish the ranges of the chemical concentrations associated with adverse effects. Such ranges allowed the estimation of preliminary effect threshold values for sediment contamination, by means of multivariate analysis. These suggested values are: Cu, 69.0; Pb, 17.4; Zn, 73.3 (mg.kg-1); PAHs, 0.5 (mg.kg-1) and PCBs, 0.1 (µg.kg-1).