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Sediments in many parts of the New York and New Jersey estuary system are contaminated with toxic organic and inorganic compounds by different sources. Because of the potential environmental consequences, detailed information on the spatial distribution of sediment contaminants is essential in order to carry out routine shipping channel dredging in an environmentally responsible way, and to remediate hot spots cost-effectively and safely. Scientific visualization and scatter data modeling techniques have been successfully applied in analyzing the sparse sampling data of sediment contaminants in New York and New Jersey estuaries, the underlying spatial characteristics of which are otherwise difficult to comprehend. Continuous realizations of contaminant concentrations in the region were obtained by using a spectral domain-decomposition scattered data model and IBM Data Explorer which is a software package for scientific data visualization.