This dataset includes field observations, bulk soil analyses, and spatially resolved elemental mapping used to evaluate the effect of transient water table dynamics on soil organic matter (SOM) amount and SOM association with soil minerals. Naturally occurring variations in the frequency of water table presence and recession from mineral soil horizons on a forested hillslope (Woodstock, NH) were used to compare soils experiencing high, medium, and low saturation cycle frequency. Within each saturation frequency category, analyses were conducted to assess bulk soil properties (e.g., total element content, pH, and extractable metals), spatial association between SOM and iron (Fe) and aluminum (Al) (using nanoscale secondary ion mass spectrometry, NanoSIMS), mechanisms of interactions between soil carbon (C) and Fe (using X-ray absorption spectroscopy (XAS) and nuclear magnetic resonance (NMR) spectroscopy), and the implications of shifting SOM-mineral interactions for SOM bioavailability and decomposition. A loss of non-crystalline Fe minerals was observed with higher saturation frequency. Further, a shift towards Al-dominated interactions was identified via increased Al/Fe ratio and Al-SOM spatial associations. These changes in SOM-mineral interaction were reflected in increased SOM bioavailability under aerobic incubation conditions for soils experiencing a legacy of high saturation frequency. Under anaerobic incubation conditions, the dissolved organic carbon (DOC) present after incubation in high saturation frequency soils also increased in bioavailability. These results underscore the need to consider the fluctuation frequency in addition to the duration of saturation events in soils. This dataset contains (1) transcribed field observations (CSV files), (2) experimental measurements (incubation experiment, bulk soil analysis, etc.), (3) NanoSIMS images (text image files), (4) XAS and NMR spectra, (5) statistical model training/testing data (CSV files), and (6) code used to analyze and plot data in this study.