Ecosystem-based approaches to aquaculture integrate environmental concerns into planning. Social-ecological systems research can improve this approach by explicitly relating ecological and social dynamics of change at multiple scales. Doing so requires not only addressing direct effects of aquaculture but also considering indirect factors such as changes in livelihood strategies, governance dynamics, and power relations. We selected the community of Puerto Morazán, Nicaragua as a case study to demonstrate how the introduction of small-scale aquaculture radically transformed another key livelihood activity, lagoon shrimp fishing, and the effects that these changes have had on lagoons and the people that depend on them. We find that shrimp aquaculture played a key role in the collapse, in the 1990s, of an existing lagoon common-property management. Shrimp aquaculture-related capital enabled the adoption of a new fishing technique that not only degraded lagoons but also led to their gradual privatization. The existence of social ties between small-scale shrimp farmers and other community members mitigated the impacts of privatization, illustrating the importance of social capital. Since 2008, community members are seeking to communally manage the lagoons once again, in response to degraded environmental conditions and a consolidation of the shrimp industry at the expense of smaller actors. This research shows that shrimp aquaculture intersects with a complex set of drivers, affecting not only how ecosystems are managed but also how they are perceived and valued. Understanding these social-ecological dynamics is essential to implement realistic policies and management of mangrove ecosystems and address the needs of resource-dependent people.