While several studies have employed Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) for analysis of complex dissolved organic matter (DOM), using FT-ICR MS to analyze molecular-level changes in labile carbon over time remains a largely unexplored area of woodchip bioreactor (WBR) design and optimization. In this study, a variety of FT-ICR MS visualization and ordination methods, such as heteroatom class distribution plots, van Krevelen diagrams, and principal component analysis, were used to explore correlations between molecular DOM properties and key WBR functions. Comparisons between upstream and downstream flow were made to elucidate possible spatial effects on lability, motivated by the potential effect of oxygen on wood-derived dissolved organic carbon. The effectiveness of periodic drying-rewetting cycles to stimulate both wood degradation by aerobic microbes and denitrification by anaerobic microbes was then explored. Analysis of DOM by FT-ICR MS presents a new way to discover how to increase the efficiency of WBRs for nitrate removal from contaminated, nitrogen-rich water sources.