Integrated classification maps were produced by combining sediment grain-size and hydrological data (water renewal time, WRT) from two Mediterranean lagoons, Lesina (LL) and Varano (LV), Italy. The geophysical characteristics of the two basins, derived from detailed bathymetric charts, are quite distinct: ∼30% of LL (mean depth ∼1 m) but only 3% of LV (mean depth ∼3 m) is shallower than 1 m. The sediments of both lagoons are mainly composed of mud (∼80%). A detailed multivariate analysis of grainsize data by EntropyMax classified the lagoon beds of LL and LV into five sedimentary facies. WRT data, computed by a hydrodynamic model, indicated different hydrological conditions in the two lagoons: LL showed a sharp west–east gradient, with a basin-wide average of ∼190 days, whilst LV showed a fairly uniform distribution and a higher basin-wide average (∼260 days). The distribution of sedimentary facies and water renewal times were combined in a composite map representing the distribution of environmental patterns. The approach outlined in this study can be used to improve zonation schemes by providing a hydromorphological perspective on transitional and coastal environments.