The current populations trapped in Neptune's main mean motion resonances in the Kuiper Belt, Plutinos in the 3:2 and Twotinos in the 2:1, contain some of the best-characterized minor objects in the solar system, given their dynamical importance. In particular, Twotinos may hide evidence of Neptune's early migration. However, these populations vary in time, declining at a rate that has not previously been clearly established. In this work, we use numerical simulations to study the long-term evolution of the Plutino and Twotino populations. We use two data sources: the most up-to-date observations and the theoretical debiased model of the Kuiper Belt known as L7. In addition to studying the giant planets' effect on these populations over 4 Gyr, we analyze the additional impact produced by the ten most massive trans-Neptunian objects (TNOs) trapped in these resonances, as well as the effect of Pluto on the 2:1 population. We find that the decay rate in each resonance can be modeled as a stochastic process well described by an exponential decay with an offset determined by an underlying long-term stable population. The most massive TNOs, particularly Pluto, influence this decay rate significantly, as expected for the 3:2 resonance. Remarkably, Pluto also strongly influences the 2:1 resonance's evolution.