We hypothesized that microbial and photochemical processing of dissolved organic matter (DOM) determines its molecular formula composition in aquatic systems to a greater degree than does the original source of the DOM. To test this hypothesis, we exposed DOM from a leachate of a wetland plant (Juncus effusus) to solar radiation or incubated it in the dark for 1.25 yr. Analysis of the extracted DOM of the leachates via Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) identified 2800 molecular formulae. Of the formulae in the initial DOM, 11% were lost during microbial decomposition in the dark and 54% under solar radiation. Solar radiation also produced a large number of formulae containing N, that were preferentially degraded by microorganisms (47% loss). We compared the “recalcitrant formulae”, i.e. those not degraded in the experiment, with those of DOM from the deep North Pacific Ocean. Of the deep sea DOM formulae, 18% were present in the recalcitrant fraction of the initial DOM. An additional 18% of the formulae in marine DOM were photoproduced and recalcitrant, and 8% were produced by microbes in the experiment. Consequently, 44% of the deep sea DOM shares identical molecular formulae with the recalcitrant DOM from the experiment, most of which were produced by the combined action of sunlight and microbes. This indicates that processes in the water column may be more important than the original source in determining the composition of bulk DOM.