This study investigated the long-term dynamics of phytoplankton communities, key environmental factors, and indicator species in Mulgeum, a major downstream site of the Nakdong River, from 1993 to 2020. Monthly phytoplankton densities ranged from 189 to 52,757,982 cells mL-1, with diatoms dominating yearround (29.1~93.4%). Notably, cyanobacteria exhibited the highest growth rates, which could exacerbate algal blooms under long-term climate change. Using generalized additive models, five environmental factorsdissolved oxygen, transparency, total phosphorus, phosphate, and discharge-were found to significantly influence monthly variations in most taxa. Cyanobacteria were most sensitive to environmental changes, while chrysophytes showed minimal dependence on specific factors. Principal component analysis grouped environmental conditions into five clusters, with each cluster characterized by distinct conditions and indicator species. A total of 122 species were identified as indicators, with green algae contributing the most. Cluster 1, characterized by high transparency and low phosphorus, was dominated by Stephanodiscus hantzschii, a common species in eutrophic waters. Cluster 4, associated with high phosphorus, highlighted Cyclotella ocellata as a key indicator, emphasizing phosphorus as a crucial determinant for diatom structure. These findings underscore the critical role of hydrological and nutrient factors in shaping phytoplankton communities and provide insights into ecological responses to environmental changes in the Nakdong River system. The results can inform sustainable management strategies to mitigate eutrophication.