The history of river inundation influences shoreline sediment biogeochemical cycling and microbial dynamics. Sediment exhibited a binary respiration response to rewetting, in which respiration from less recently saturated sediment was suppressed relative to more recently saturated sediment, likely due to inhibition of fungal metabolic activity. River shorelines should likely be integrated as a distinct environment into hydrobiogeochemical models to predict watershed biogeochemical function.