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A Novel Community Engaged System Thinking Approach to Controlling Nutrient Pollution in the Belize Cayes Nutrient pollution (anthropogenic discharge of nitrogen and phosphate) is a major concern in many parts of the world. Excess nutrient discharge into nutrient limited waters can cause toxic algal blooms that lead to hypoxic zones, fish die-offs, and overgrowth on reefs. This can lead to coral reefs being more vulnerable to global warming and ocean acidification. For coastal communities that depend of fishing and tourism for their livelihood, and for reefs to protect coastlines, these effects can be devastating. A major source of nutrient input into the aquatic environment is poorly treated wastewater from Onsite Wastewater Treatment Systems (OWTS). When properly sited, built, and maintained conventional OWTS are great for removing fats, grease, biological oxygen demand (BOD), and total suspended solids (TSS), but they are rarely designed for nutrient removal and commonly have high nutrient levels in their effluent. This study investigates the factors that influence the performance of OWTS, the Caribbean region’s most common type of treatment technology, in the Belizean Cayes where salt water flushing is common. Using mass-balance-based models for existing and proposed OWTS to predict the system’s performance under various conditions, along with OWTS’ owner, maintainer, and user input, a novel community engaged system thinking approach to controlling nutrient pollution will be developed. Key model performance metrics are concentrations of nitrogen species, BOD, and TSS in the effluent. To demonstrate the model’s utility, a sensitivity analysis was performed for case studies in Belize, estimating the impact on nutrient removal efficiency when changes are made to variables such as number of daily users, idle periods, tank number and volume, oxygen concentration and recirculation. For the systems considered here, strategies such as aeration, increased biodigester tank size, addition of aerobic and anoxic biodigesters, recirculation, addition of a carbon source, ion exchange media is predicted to decrease the effluent nitrogen concentration, and integration of vegetation for nutrient uptake both on land and in the nearshore environment. In a previous case, the addition of an aerator was predicted to decrease the effluent ammonium concentration by 13%, whereas increasing the biodigester tank size would only decrease the effluent ammonium concentration by ~7%. Model results are shared with system manufacturers and operators to prioritize possible modifications, thereby optimizing the use of finite resources, namely time and money, for costly trial-and-error improvement efforts.