A mathematical model (ALaRM) for predicting the reacidification profile of calcium carbonate treated lakes has been calibrated and confirmed using data from two Lake Acidification Mitigation Project (LAMP) lakes. This manuscript focused on the use of ALaRM to evaluate the relative impact of bottom sediment processes on the reacidification rate of the LAMP lakes. Prior to liming the lakes exhibited annual average sediment-to-water ANC fluxes of 194 and 240 meq/m2-yr for Woods Lake and Cranberry Pond, respectively. Following liming there was a period of net water-to-sediment ANC flux due to a reversal of the gradients of ANC-determining chemical species, indicating a buffering effect of bottom sediments on water column acid-base chemistry. A sensitivity analysis indicated that calcite treatment of sediments as well as the water column could mitigate the sediment reacidification-accelerating effect.