Mexico’s Atlantic Coast with its mosaic of coastal wetlands is vulnerable to sea level rise. These wetlands are transition zones between the terrestrial and the marine environments. Due to their location, the rise in sea level could increase the level of flooding and salinity in these ecosystems. A synthetic model was applied to the Mexican Atlantic coast, and the La Mancha lagoon was used for local experiments with wetland species. Our objectives were: 1) identify the potentially floodable coastal wetlands in the face of a sea level rise of one and two meters, and 2) determine the percentages of germination for seven popal (freshwater marsh) species and the survival and growth of a swamp tree species, Annona glabra seedlings under different flood and salinity conditions. For the first objective, we developed a synthetic model using three information layers: altitude of the land (elevation), water bodies, and wetland vegetation. For the second, we carried out two experiments: 1) a laboratory germination experiment with eight treatments (2 flood levels × 4 salinity levels), and 2) greenhouse growth seedlings experiment with nine treatments (3 flood levels × 3 salinity levels). Our model identified 470,480 and 720,902 ha of wetlands potentially affected under one- and two-meter scenarios, respectively. The germination experiment results showed that most popal species germinated higher under no salinity conditions as expected. The seedling experiment recorded that survival and growth were higher under no salinity conditions. In both experiments, salinity was the most stressful factor. According to the model, the tulares and mangroves will have significant areas affected by sea level rise. In addition, freshwater wetlands will be affected in two crucial stages of their cycle life: germination and seedlings establishment