Organisms are embedded in environments, with which they engage in an ongoing two-way interaction called structural coupling. It is in this context that an organism develops, behaves, thrives, and ultimately dies. This paper introduces a network-based methodology for analyzing how an organism and environment unfold together through structural coupling, and demonstrates this methodology in a cellular Potts model. A morphology-environment transition network consists of all reachable combinations of morphological and environmental states as its nodes, and the transitions between these morphology/ environment states as its edges. In a given simulation, the model cell and its environment move through this network as both dynamically unfold. Analysis of such a network reveals several interesting properties, including attractor states, divergence of network structure when the cell is placed in different environments, and niche construction in which the cell’s influence over its environment increases its own viability.