Urban wetlands play an increasingly crucial role, and the health assessment of their ecosystems is an important process that helps us understand the current condition of wetlands and take appropriate protective measures. To explore the ecological health status ofthe Lhalu Wetland and its relationship with water environmental factors, phytoplankton samples were collected and water environmental factors were measured in the main water systems of Lhalu Wetland in July (summer), October (autumn) 2021, and May (spring) 2022. Phytoplankton species were identified, and their cell abundance and biomass were calculated. The ecological health status of the wetland was evaluated using the morphologically-based functional group (MBFG), water quality index (WQI), and phytoplankton index of biotic integrity (P-IBI). The spatiotemporal distribution characteristics of water quality and morphologically-based functional group, and the correlation between P-IBI values and water environmental factors were analyzed. The research results showed: (1) Based on the WQI values, the overall water quality of Lhalu Wetland was evaluated as “good” to “moderate” with spatial and temporal variations in water quality: it was best in spring, followed by autumn, and worst in summer, and the eastern part was better than the western part. (2) Based on the P-IBI values, the overall water ecological health status of Lhalu Wetland across three seasons was evaluated as “health” to “sub-health”, with the spring water ecological health status being superior to autumn, which was superior to summer, and the central-eastern sampling points were generally superior to the south-western and north-eastern parts. (3) The P-IBI values showed a significant positive correlation with the WQI values, and the evaluation of the water ecological health status of Lhalu Wetland based on P-IBI was closely consistent with the results of WQI evaluation. Dissolved oxygen was the main water environmental factor affecting the water ecological health status of Lhalu Wetland, and temperature, water volume, human activities, and land use types were important factors affecting the water quality and water ecological health status of Lhalu Wetland. (4) In spring, the abundance of functional groups Ⅰ and Ⅲ increased as the water ecological health status of Lhalu Wetland declined. In summer, the ecological health status of the water body had little relationship with the changes in the abundance of functional groups. In autumn, the increase in the abundance of functional groups Ⅲ and Ⅶ was significantly associated with the decline in the ecological health status of the water body.