Complexity theory proposes that spatial self-organization, the process whereby small-scale, localized interactions among the components of a system generate complex spatial structures at large spatial scales, explains the formation of autogenic spatial patterns in ecosystems. We question this premise by reviewing three estuarine ecosystems – mussel beds, mudflats and salt marshes – where self-organization has been put forward to explain spatial patterns. Our review highlights that these self-organized estuarine systems are shaped by the combination of small-scale interactions between ecological and physical processes on the one hand, and large-scale physical forcing on the other. More specifically, local interactions generate patchiness at small spatial scales, whereas landscape forcing determines the shape and orientation of these patches in the landscape. We present a framework that illustrates how self-organized ecosystems are shaped by interactions between organisms and physical processes occurring at multiple spatial scales. Moreover, the present review of estuarine systems underlines that scale-dependent feedbacks are capable of explaining spatial patterns that are much more complex than the regular patterns to which they have been applied so far.