The chinampas (raised beds) of Xochimilco, Mexico City, are highly productive, traditional wetland agricultural systems, which were able to feed most of the population in pre-hispanic times. There is a strong trend to substitute chinampas with plastic greenhouses for flower production, which creates negative impacts in the landscape, environment and culture. This study compares the environmental and socio-economic sustainability of chinampas and greenhouses, at both the farm and regional levels, using the MESMIS framework. Even though the results show that greenhouses are more profitable, the contribution of chinampas to ecosystem services cannot be substituted by greenhouses, as tree cover is lost, canals are filled and food is not provided. Greenhouses had a higher diversity, but also a higher agrochemical use and are heavily dependent on external inputs and subsidies. Chinampas have shifted from staple crops to commercial horticulture in order to remain a technically viable and economically feasible option for local farmers. However, compensation mechanisms for the provision of ecosystem services are urgently needed if this ancient system is to be maintained. The framework allowed the integration of indicators at both farm and regional scales, combining on-farm surveys with GIS techniques, which could assist in ecosystem service valuation.