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Respiration in frozen soils is limited to thawed substrate within the thin water films surrounding soil particles. As temperatures decrease and the films become thinner, the available substrate also decreases, with respiration effectively ceasing at −8 °C. Traditional exponential scaling factors to model this effect do not account for substrate availability and do not work at the century to millennial timescales required to model the fate of the nearly 1100 Gt of carbon in permafrost regions. The exponential scaling factor produces a false, continuous loss of simulated permafrost carbon in the 20th century and biases in estimates of potential emissions as permafrost thaws in the future. Here we describe a new frozen biogeochemistry parameterization that separates the simulated carbon into frozen and thawed pools to represent the effects of substrate availability. We parameterized the liquid water fraction as a function of temperature based on observations and use this to transfer carbon between frozen pools and thawed carbon in the thin water films. The simulated volumetric water content (VWC) as a function of temperature is consistent with observed values and the simulated respiration fluxes as a function of temperature are consistent with results from incubation experiments. The amount of organic matter was the single largest influence on simulated VWC and respiration fluxes. Future versions of the parameterization should account for additional, non-linear effects of substrate diffusion in thin water films on simulated respiration. Controlling respiration in frozen soils based on substrate availability allows us to maintain a realistic permafrost carbon pool by eliminating the continuous loss caused by the original exponential scaling factors. The frozen biogeochemistry parameterization is a useful way to represent the effects of substrate availability on soil respiration in model applications that focus on century to millennial timescales in permafrost regions.