During four decades, the Ria de Aveiro was subjected to the loading of mercury from a chlor-alkali industry, resulting in the deposition of several tons of mercury in the sediments. The present study evaluates the impact of this disturbance and the recovery processes, temporally and spatially, by means of examining the richness of the species of salt marsh plants and mercury concentrations in sediments over the last fifty years. The temporal assessment showed that the mercury loading induced a shift in the species composition of the salt marsh from a non-disturbed salt marsh with higher species richness to an alternative state dominated by Phragmites australis. The horizontal assessment, through a mercury gradient, presents the same trend, indicating that P. australis is the species most tolerant to higher mercury concentrations, comparative to Halimione portulacoides, Arthrocnemum fruticosum, Triglochin maritima, Juncus maritimus and Scirpus maritimus. After the reduction of mercury discharges in 1994, the salt marsh shows a slowly return path recovery response. The hysteresis in the response results in the temporal gap between the reduction in mercury concentrations in the sediment and the salt marsh species richness response, comparatively to the existing diversity in the local reference marsh.