An empirical model based on an ecohydrological approach was developed, which allows the integration of hydrographical, topographical and physicochemical information with vegetation characteristics of mangroves and marshes of the Bragança Peninsula, North Brazil. A synoptic distribution of sediment porewater salinity was produced with isolines derived from predicted porewater salinity values from a GIS-based, multiple regression model. It includes a non-linear function of calculated inundation frequencies, the measured salinity distribution in the adjacent estuaries and sediment porewater salinities determined in the dry season. An excellent fit between measured and predicted porewater salinities was obtained. Highly significant correlations were found between vegetation height, inundation frequency and predicted porewater salinities. The relationship between vegetation height and predicted porewater salinities indicated the existence of at least three data ‘clusters', which probably respond to different height to diameter-in-breast-height proportions according to age and environmental stress conditions. The porewater salinities produced by the model proved to be a solid proxy for the average stress situation of mangrove vegetation. The model offers good potential as a tool for analysing wetland dynamics, particularly at a synoptic, basin level.