San Quintin, Mexico, provides a useful site for integrated analyses of material fluxes and socioeconomic constraints in a geographically isolated system. Natural resource utilization on the land is dominated by groundwater exploitation for cultivation of horticulture crops (primarily tomatoes). Irrigation exceeds water recharge minus export by a factor of 6. Resource utilization in the bay is dominated by oyster culture; food for the oysters is provided by tidal exchange of bay and ocean water. Consideration of oyster respiration and system respiration suggests that the present level of aquaculture is about 40% of the sustainable level. A “physical unsustainability index” (PhUI) was developed to measure the proportional departure of utilization of the most limiting resource for sustainability: 6 on land; 0.4 in the bay. Based on PhUI and measures of economic development, we conclude that aquaculture is more viable than agriculture.