Coastal ecosystems play a key role in the transformation, transport, burial and exchange of water and organic and inorganic carbon and nitrogen between land, atmosphere and the ocean. With an overwhelming majority of the human population living in the coastal zone, coastal ecosystems are among the most heavily impacted ecosystems in the world. Like many other coastal regions, the Plum Island Ecosystem region, which lies just north of Boston, Massachusetts, is experiencing population growth in the watershed, land use change, climate change, altered hydrologic cycles, and sea level rise. The Plum Island Ecosystems (PIE) LTER is an integrated research, education and outreach program whose goal is to develop a predictive understanding of the long-term response of a coupled watershed and estuarine ecosystem to changes in climate, land use and sea level and to apply this knowledge to the wise management and development of policy to protect the natural resources of the coastal zone. The program is carrying out long term observations and process studies in the watersheds, marsh, and estuary to determine how several aspects of global change influence organic matter and inorganic nutrient biogeochemistry and estuarine food webs. Modeling is an essential component of the LTER program used to integrate both within and across programmatic areas.