Estuarine modification of terrestrial and riverine/estuarine organic matter may strongly affect the eventual preservation of reduced carbon in world oceans and is also important in nutrient and contaminant cycling. In this study multiple size classes of organic matter (including particles and dissolved fractions, POM and DOM) from a transect down the Delaware River/Bay system were collected and analyzed. Variations in chemical characteristics were identified using direct temperature-resolved mass spectrometry (DT-MS) and wet chemical techniques coupled with discriminant analysis and canonical correlations analysis. These comparative measures illustrate the complementary nature of traditional versus more recent mass spectrometry approaches. Within the estuary system, organic matter size class, rather than sample location, is found to be the major source of molecular-level variation. POM is enriched in proteins, nucleic acids, fatty acids, chlorophyll, and sterols, whereas DOM is enriched in aminosugar, furfural, and alkylphenol moieties. In positive ammonia chemical ionization DT-MS studies, which focus on the sugar components in POM and DOM, riverine very high molecular weight DOM (>30 kDa, <0.2 μm) is found to be enriched in deoxysugars and methylsugars compared to all other estuarine and coastal samples.