Self-organized spatial patterns have been proposed as possible indicators for regime shifts in ecosystems. Until now, this hypothesis has only been tested in drylands. Here, we focus on intertidal mudflats where regular spatial patterns develop in early spring from the interaction between diatom growth and sedimentation but disappear when benthic herbivore abundance increases in early summer, accompanied by a dramatic shift to a bare mudflat. We followed the patch-size distributions of diatom biofilms during this degradation process. As time progressed, we found a temporal change in the spatial configuration occurring simultaneously with the loss of the diatom–sediment feedback. This indicates a gradual failure in time of the self-organization process that underlies regular patterning in this ecosystem. The path to degradation co-occurred with the loss of the larger patches in the ecosystem, which resulted in a decrease of the truncation in the patch-size distribution. Hence, our study in mudflat ecosystems confirms the general hypothesis that spatial patterns can provide important clues about the level of degradation. Nevertheless, our study highlights the need for thorough study about the type of spatial patterns and the nature of the underlying feedbacks before a reliable assessment of ecosystem status can be made, as changes in patch-size distribution differed markedly with those observed in other ecosystems.