Indirect effects appear to play a significant role in the organization and transformation of complex adaptive systems (CAS). In ecosystems, one type of CAS, organisms and their environments are coupled by an intricate network of energy, matter, and information exchanges. This makes it possible for one species to affect the distribution, abundance, and behavior of other species without direct contact. Because we do not fully comprehend factors controlling the development and propagation of indirect effects through the interaction networks of CAS, we cannot predict their importance a priori. The overarching goal of the research presented in this dissertation is to develop a better understanding of processes that create, constrain, and sustain ecological systems. The research focuses on the role of ecosystem architecture (structure and function) in the development and propagation of environ indirect effects, which result from energymatter transactions. In Chapters 2 and 3 we distinguish the role of biodiversity and the number and pattern of interactions in creating indirect pathways. In the process, we reveal a form of hierarchical organization based on strongly connected components. In Chapters 4 and 5, we examine how the distribution of energymatter flux across a fixed structure influences the magnitude of