Santa Cruz Island is arguably the most visited island in the Galapagos. The coastal zone of Puerto Ayora, Academy Bay, Santa Cruz Island is susceptible to changes from land-ocean interactions, climate shifts and human activities. Human activities from urbanization, tourism and waste production are altering nitrogen and phosphorus nutrient levels in groundwater and along this coastline. The ecosystem metabolism of the coastal waters is sensitive to these human activities. Direct and indirect anthropogenic influences were examined within Academy Bay. Data sources were sparse. Relevant data were obtained during 2005-2006. The Land Ocean Interaction Coastal Zone (LOICZ) methodology was used to quantify the water-salt and nutrient budgets for Academy Bay. The hydrographic budget described inputs and outputs within this system, and was used to determine the salinity and residence time. Dissolved inorganic nitrogen (DIN) and dissolved inorganic phosphorus (DIP) nutrient budgets were used to determine the net ecosystem metabolism (NEM) equation, which defines a system as a source or a sink. DIN and DIP concentrations revealed that the NEM is autotrophic dominated by primary producers. The targeted area is also a sink for DIN and DIP. The Pressure-State-Impact-Response (PSIR) assessment was used to identify socio-ecological stresses; through which it was determined that tourism and urbanization highly affect nutrient concentrations. An increase in these stresses may induce state changes and result in impacts such as eutrophication and algal blooms (toxic or non-toxic). The PSIR and budget analyses may be used as a framework to advise on coastal management and policy.