While the spatiotemporal dynamics of phytoplankton community structures in river ecosystems have been extensively studied, their primary driving factors remain elusive, particularly at the watershed scale. This research examined the phytoplankton community structure across three watersheds of an island and concurrently analyzed its response to water level fluctuations (WLFs). The phytoplankton density was notably higher at elevated water levels, registering an increase of 1.29 times in Nandu River, 1.34 times in Changhua River, and 1.28 times in Wanquan River. Notably, the middle reaches of the Changhua River recorded the highest phytoplankton density (4.46 × 108 cells/L). Broadly speaking, Cyanophyta, Chlorophyta, and Bacillariophyta remained the predominant phytoplankton across varied water levels. Dominant phytoplankton species varied with water levels; however, the most prevalent species consistently belonged to the Cyanophyta group, primarily Microcystis or Merismopedia, with dominance ranging between 0.17 to 0.38 (low water level) and 0.18 to 0.32 (high water level). Enhanced phytoplankton diversity and richness were observed at higher water levels, correlating with increased concentrations of NH4+-N, NO3−-N, and PO43− in the river water. Consequently, nutrient fluctuations driven by hydrodynamics significantly influence the phytoplankton community structure in island river ecosystems.