The Mississippi River and some of its tributaries were sampled for natural organic substances dissolved in water and in suspended and bed sediments during seven sampling cruises from 1987-90. The sampling cruises were made during different seasons, in the free-flowing reaches of the river from St. Louis, Missouri, to New Orleans, Louisiana. The first three cruises were made during low-water conditions, and the last four cruises during high-water conditions. The purpose for sampling and characterizing natural organic substances in the various phases in the river was to provide an understanding of how these substances facilitate contaminant transport and transformations in the Mississippi River. Significant conclusions of this study were: (1) Natural organic substances appear to stabilize ' certain colloids against aggregation; therefore, these colloids remain in suspension and can act as transport agents that are not affected by sedimentation. Bacteria were found to be a significant fraction of organic colloids. (2) A new class of organic contaminants (polyethylene glycols) derived from nonionic surfactant residues was discovered dissolved with natural organic substances in water. These polyethylene glycols have the potential to affect both organic and inorganic contaminant transport in water. (3) The entire dissolved organic-matter component under varying hydrologic and seasonal conditions was characterized. (4) A method was developed to characterize organic matter in sediment by solid-state, 13C-nuclear magnetic resonance spectrometry. (5) The organic matter in suspended sediments was characterized by a variety of spectral and nonspectral methods. The protein component (significant in trace-metal binding) and lipid component (significant in organic-contaminant binding) were found to be major constituents in natural organic matter in suspended sediment. (6) Pools are reservoirs acting as traps of sedimentary organic matter of allochthonous origin and export material of autochthonous nitrogen. (7) A major portion of the mass of organic colloids in transport consisted of bacterial cells.