Boujagh National Park, with water ecosystems including Boujagh and Kiashahr wetlands, has an area of approximately 3477.3 hectares. In order to study factors affecting the vegetation in aquatic and wet habitats, 44 releves were implemented in the region. To test the chemical properties of the available water, samples were collected from 22 releves. The results of a two-way species indicator analysis of the modified TWINSPAN suggested that four groups of plants were present in the region. The first group being floating, immersed and submerged and the third and fourth groups being mostly helophytic. The second group of plants grows in areas with sand and mud. The results of comparative DCA analysis of water factors (PH, Depth, P, N, Cl, CO₃, Hco₃, EC, Na, K) showed a significant correlation between the factors and plant groups and the most important factors influencing the distribution and separation of plants was found to be water depth. In addition, Boujagh and Kiashahr wetlands vegetation map, based on the plant groups, was also prepared.