Rapid coastal development poses significant challenges to the sustainability of small-scale fisheries, tourism, and coastal ecosystems. This study develops an adaptive coastal management framework through integrated capacity and network-based assessments. Specifically, it aims to (1) evaluate the social, economic, and ecological capacities of coastal systems in Yogyakarta, Indonesia, using the Capacity Index of Sustainable Coastal Development (CISCD) and examine their interrelationships through Spearman correlation, and (2) identify the synergy–trade-off network among sustainability themes using the Hyperlink-Induced Topic Search (HITS) algorithm to support adaptive coastal management. Data were collected through field surveys, interviews, and focus group discussions involving 64 stakeholders, including fishers, aquaculture farmers, tourism operators, local traders, and government officials, complemented by a spatial analysis of land-use change from 1990 to 2025. The CISCD framework was constructed using seven sustainability themes and integrated with correlation and network analyses. All themes exhibited positive correlations, although their structural roles varied among regencies. Standard of living emerged as the principal trade-off hub in Bantul and Kulon Progo (hub score = 1.00), whereas population pressure was the dominant trade-off driver in Gunungkidul (hub score = 1.00), accompanied by high fisheries productivity centrality (hub score = 0.86). In contrast, institutional quality and the blue economy consistently functioned as key synergy drivers reflecting regional geomorphological and livelihood characteristics. The integrated assessment framework identifies regional leverage points for adaptive coastal management by supporting spatial zoning, institutional collaboration, livelihood diversification, and ecosystem-based coastal planning.