In this paper, we expand existing conceptual tools from institutional analysis and common-pool resource theory to guide research on self-governing regimes. We use small-scale fisheries as an illustrative case of complex systems that take place largely outside of the reach of State authority. While most common-pool resources theory has focused on harvesting activities to date, small-scale fisheries are organized around interlinked pre-harvesting, harvesting, and post-harvesting activities forcing us to rethink an approach to better understand operational fishing activities. To do this first, we propose a new institutional level, the micro-institutional level, that captures how individual behavioral patterns shape self-organization. Then, we describe a basic set of linked action situations common to all small-scale fisheries that capture the connections among pre-harvesting, harvesting, and post-harvesting decisions. We illustrate the utility of these theoretical advancements with an empirical investigation of self-governing fisher-fish buyer relationships in Mexican small-scale fisheries.