Ultrahigh resolution electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS) has proved essential for the complete separation of the thousands of peaks present in natural organic matter (NOM), a complex assemblage of organic molecules present in water, soils, and sediments. An improved understanding of its composition is crucial to understand how pollutants interact with NOM and how NOM cycles through global carbon cycles. Optimizing the acquisition and handling of the FTICR mass spectra is the first step to obtaining high quality data. A simple method to internally calibrate the peaks in the complex spectra, using naturally present fatty acids, is demonstrated. Furthermore, a method was developed to directly analyze natural waters with low dissolved organic carbon (DOC), by utilizing sequential selective ion accumulation (SSIA), which decreases the baseline noise while increasing signal to noise ratios. Once optimization is achieved, ESI-FTICR-MS is applied to characterize dissolved organic matter (DOM) as it is transported along a river to ocean transect of the lower Chesapeake Bay. To evaluate the advantages of using direct analysis, a C18 extract of riverine water is compared to its whole, unfractionated water. Along this transect, the DOM tends to become more aliphatic and contain lower abundances of oxygen-rich molecules as one progresses from inshore to the offshore. Next, multivariate statistics, such as hierarchal cluster analysis (HCA) and principal component analysis (PCA), are utilized to explore the large datasets acquired from DOM mass spectra. PCA deciphers which of the thousands of formulas are significant to particular samples, and then van Krevelen diagrams highlight what types of compounds are molecular signatures to the samples. A considerable amount of formula overlap exists between samples along the transect, but having identical molecular formulas does not necessarily indicate the same molecular structure. Taking advantage of the tandem mass spectrometry (MS/MS capabilities, I isolate and fragment ions in the DOM. The MS/MS fragmentation pattern obtained for selected peaks are strikingly similar in the terrestrial and saline bay DOM, leading us to believe that the compounds have similar structural entities. Based on the functionalities lost during the fragmentation, a lignin-derived structure fits the molecular formulas best. Overall, ESI-FTICR-MS is a powerful technique for the investigation of DOM and has the ability to detect compositional variations along the river to ocean transect. Further use of ESI-FTICR-MS will clearly lead to additional future advancements in the areas of aquatic, soil, and analytical chemistry.