There are substantial uncertainties in the computational models currently used to predict the heating environment and the Thermal Protection System material response during Mars entry. Flight data are required to quantify and possibly reduce such uncertainties as well as improve current computational tools. The Mars Science Laboratory Entry, Descent, and Landing Instrumentation suite will provide a comprehensive set of flight data that will include subsurface temperature measurements of its Phenolic Impregnated Carbon Ablator heatshield at different locations. The purpose of this paper is to investigate the time-dependent estimation of Mars Science Laboratory surface heating from simulated Mars Science Laboratory Entry, Descent, and Landing Instrumentation temperature data using inverse methods in the presence of random and bias measurement and model errors. The surface heat flux is indirectly reconstructed by estimating the discretized heat transfer coefficient profile as a function of time. Whole-time domain least-squares methods in conjunction with the Tikhonov regularization technique are applied to this problem. The performance of the estimation methods and the accuracy of the reconstructed surface conditions are investigated under different types of errors in the measurements, such as random noise and thermocouple lag. Furthermore, the effect of material property bias on the estimation of surface conditions is also studied.