This study explores the functional relationship between model physics parameters and model output variables for the purpose of 1) characterizing the sensitivity of the simulation output to the model formulation and 2) understanding model uncertainty so that it can be properly accounted for in a data assimilation framework. A Markov chain Monte Carlo algorithm is employed to examine how changes in cloud microphysical parameters map to changes in output precipitation, liquid and ice water path, and radiative fluxes for an idealized deep convective squall line. Exploration of the joint probability density function (PDF) of parameters and model output state variables reveals a complex relationship between parameters and model output that changes dramatically as the system transitions from convective to stratiform. Persistent nonuniqueness in the parameter–state relationships is shown to be inherent in the construction of the cloud microphysical and radiation schemes and cannot be mitigated by reducing observation uncertainty. The results reinforce the importance of including uncertainty in model configuration in ensemble prediction and data assimilation, and they indicate that data assimilation efforts that include parameter estimation would benefit from including additional constraints based on known physical relationships between model physics parameters to render a unique solution.