Self-organized spatial patterns are increasingly recognized for their contribution to ecosystem functioning, in terms of enhanced productivity, ecosystem stability, and species diversity in terrestrial as well as marine ecosystems. Most studies on the impact of spatial self-organization have focused on systems that exhibit regular patterns. However, there is an abundance of patterns in many ecosystems which are not strictly regular. Understanding of how these patterns are formed and how they affect ecosystem function is crucial for the broad acceptance of self-organization as a key-stone process in ecological theory. Here, using transplantation experiments in salt-marsh ecosystems dominated by Scirpus mariqueter, we demonstrate that scale-dependent feedback is driving irregular spatial pattern formation of the vegetation. Field observations and experiments revealed that this self-organization process affects a range of plant traits (the distributions of orientations, nodes number and distances) as well as enhances vegetation productivity, and that patchiness in self-organized saltmarsh vegetation can support a better micro-habitat for macrobenthos, promoting their total abundance and spatial heterogeneity of species richness. Our results extend the existing concepts of self-organization and its effects on productivity and biodiversity to the spatial irregular patterns that are observed in many systems. Our work also helps to link between the so-far largely unconnected fields of self-organization theory and trait-based, functional ecology.