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Abstract Recent experiments and field observations have indicated that biomarker molecules can react over short timescales relevant to seismic slip, thereby making these compounds a useful tool in studying temperature rise in fault zones. However, short‐timescale biomarker reaction kinetics studies have previously focused on compounds that have already experienced burial heating. Here, we present a set of hydrous pyrolysis experiments on Pleistocene‐aged shallow marine sediment to develop the reaction kinetics of long‐chain alkenone destruction, change in the alkenone unsaturation ratio (), and change in then‐alkane chain length distribution. Our results show that biomarker thermal maturity provides a useful method for detecting temperature rise in the shallow reaches of faults, such as subduction zone trench environments. Through the course of our work, we also noted the alteration of total alkenone concentrations andvalues in crushed sediments stored dry at room temperature for durations of months to years but not in the solvent extracts of these materials. This result, though parenthetical for our work in fault zones, has important implications for proper storage of sedimentary samples to be used for alkenone paleotemperature and productivity analysis.