A new method to evaluate archaeological wetland sites in a more objective way was tested. Different wetland environments have been sampled in areas of a nature reserve and their macroremain content analysed to build a modern analogue dataset. This dataset was then used to characterise archaeological samples from a navigation channel from the Roman port city Lattara. In the modern analogue samples, the different wetland types (saline/brackish or fresh water) could be differentiated in the correspondence analysis. Within these groups, the sampled area of the littoral (submerged, shoreline, unsubmerged) could also be differentiated. This dataset can therefore provide a basis for the interpretation of the nature and degree of aquatic influence and layer formation processes in archaeobotanical records of coastal sites. In the tested archaeological samples from the navigation channel of Lattara, changes in space and time could be tracked using the modern analogue dataset and geoarchaeological information. The channel lost its fresh water supply and silted up over a short period of time (approx. 100 years).