In this paper, we consider the efficient estimation of local boiling heat fluxes from transient temperature measurements in the heater close to the heater surface. For accurate prediction, heat flux estimation is formulated as a transient three-dimensional (3D) inverse heat conduction problem (IHCP). This inverse problem is ill-posed and cannot be treated straightforwardly by established numerical methods. In order to obtain a regularized stable solution, a large-scale time-dependent PDE-constrained optimization problem has to be solved and an appropriate stopping criterion for the termination of the iterative solution process has to be chosen. Since the boiling heat flux is non-uniformly distributed on the heater surface due to the strong local activity of the boiling process, the use of a fixed uniform spatial discretization is not efficient. Instead, an adaptive mesh refinement strategy can be used to obtain an appropriate discretization which significantly reduces the total computational effort. In this work, we present an automatic algorithm incorporating an adaptive mesh refinement via a heat flux-based a-posteriori error estimation technique. The suggested algorithm can cope with both spatially point-wise or highly resolved temperature observations efficiently. It is applied to real measurement data obtained from two different types of pool boiling experiments. The numerical results show that the computational effort can be reduced significantly for given estimation quality. This adaptive IHCP solution technique can be also viewed as an efficient soft sensor to deduce unmeasurable local boiling heat fluxes.