We propose and analyse a posteriori estimates for global-in-time, nonoverlapping domain decomposition methods for heterogeneous and anisotropic porous media diffusion problems. We consider mixed formulations, with a lowest-order Raviart–Thomas–Nédélec discretization, often used for such problems. Optimized Robin transmission conditions are employed on the space-time interface between subdomains, and different time grids are used to adapt to different time scales in the subdomains. Our estimators allow to distinguish the spatial discretization, the temporal discretization, and the domain decomposition error components. We design an adaptive space-time domain decomposition algorithm, wherein the iterations are stopped when the domain decomposition error does not affect significantly the global error. Thus, a guaranteed bound on the overall error is obtained on each iteration of the space-time domain decomposition algorithm, and simultaneously important savings in terms of the number of domain decomposition iterations can be achieved. Numerical results for two-dimensional problems with strong heterogeneities and local time stepping are presented to illustrate the performance of our adaptive domain decomposition algorithm.