Several studies investigated the dynamics of coastal areas, investigating some issues such as sea-level rise, floods, and water scarcity. Despite existing studies discussing coastal areas, there are limited studies investigating Asian coastal areas and their proposed solutions may not overcome extreme events. This study investigates the dynamics of the Pekalongan coastal area, Central Java, Indonesia. Despite efforts such as the development of dikes and groundwater pumping, people in Pekalongan have currently experienced more frequent floods and land subsidence that have led to larger inundated areas and people migration. Using the system archetypes, this study shows that the coastal area consists of renowned nexus elements (water, land, and food) and less recognized nexus elements (health and wellbeing). This means that changes in one nexus element may threaten other nexus elements, exacerbating problems in the observed system. For instance, unsustainable nexus actions such as overexploited groundwater tend to increase flooded areas, threatening people health, and inducing people migration. The system archetypes also show that the coastal area consists of Limits to Growth structures. As such, growth engines such as land-use change and groundwater pumping should be managed or restricted properly. Managing growth engines can prevent us from natural disasters such as floods and water scarcity. Likewise, as the system archetypes describe generic patterns and solutions, some findings of this study can be useful for the other coastal areas.