In wetland ecosystems, small shallow lakes are critical transition zones of land and water, which are usually dominated by aquatic plants with different growth forms. However, the differences and key influencing factors of phytoplankton communities in shallow lakes dominated by different aquatic plants are unclear. On this basis, nine surveys were conducted at five sampling sites of three lakes in Zhangye National Wetland Park from June to November in 2022, which were respectively dominated by the emergent Phragmites australis （LL）, the submerged Potamogeton perfoliatus （CL）, and the floating-leaved Nymphaea tetragona （SL）. During the study period, the three lakes showed obvious habitat differences. A total of 237 species of phytoplankton in seven phyla and 93 genera were identified in the three lakes, including 189 species, 151 species, and 147 species in the LL, CL, and SL lakes, respectively. Among them, Ulnaria acus, Scenedesmus quadricauda, Achnanthidium minutissimum, Nitzschia stagnorum, Navicula radiosa , and Gymnodinium aeruginosum were shared dominant species of all three lakes, indicating that they had strong environmental adaptability, whereas Navicula lanceolala , Encyonopsis cesatii , and Eunotia diodon and Cymbella aequalis were only dominant in the CL, LL, and SL lakes, respectively. Simultaneously, these dominant algae appeared with obviously distinct statuses of niche width, niche overlap, and interspecific correlation among the three lakes. Using principal coordinate analysis （PCoA） and permutational multivariate analysis of variance （PERMANOVA）, significant differences were found in algal community composition among the three lakes （ P <0.001）. Multiple regression on （dis）similarity matrices analysis （MRM） showed that the heterogeneity of phytoplankton communities among the three lakes was positively affected by NO 3 - -N and pH and negatively affected by dissolved oxygen （DO） and was closely positively correlated with the abundance of six dominant species, namely, S. quadricauda , U. acus , N. stagnorum , Pseudoanabaena sp., Merismopedia punctata , and A. minutissimum . These results indicate that aquatic plants with different growth types could affect the composition, structure, and stability of phytoplankton communities in the same habitat with them by shaping their habitat heterogeneity. Therefore, selecting specific growth types of aquatic plants for aquatic ecosystem restoration in wetland construction and management will be conducive to regulate the state of water habitat and phytoplankton community structure effectively.