Phytoplankton are widely acknowledged as sensitive and effective bioindicators for water quality assessment due to their rapid and quantifiable responses to environmental changes. This study assessed the performance of two phytoplankton-based indices: Palmer’s Algal Pollution Index (API) and the Applied Algal Research Laboratory–Phytoplankton Score (AARL-PP). Water samples were collected from 264 sites across 50 lentic water bodies in four regions of Thailand during April and May 2024, and analyzed for chlorophyll-a (µg/L), total nitrogen (TN, µg/L), and total phosphorus (TP, µg/L). The results show that the mean API scores (± SD) across trophic categories were oligotrophic = 27, mesotrophic = 16 ± 7.11, eutrophic = 18 ± 6.26, and hypereutrophic = 16 ± 6.51. Corresponding AARL-PP scores were oligotrophic = 7.67, mesotrophic = 6.00 ± 1.23, eutrophic = 7.37 ± 1.01, and hypereutrophic = 7.40 ± 0.84. Although API values showed no significant differences among trophic groups (Tukey’s HSD test), suggesting limited sensitivity to nutrient gradients, AARL-PP scores demonstrated significant distinctions between mesotrophic and both eutrophic and hypereutrophic systems. Furthermore, AARL-PP exhibited a stronger correlation with the Trophic State Index (TSI) (R² = 0.0946) than API (R² = 0.045). As one of the first large-scale, regionally diverse comparisons of phytoplankton indices and nutrient-based indicators in tropical lentic ecosystems, this study addresses a critical research gap by integrating chemical and biological assessments and applying a locally developed index. The findings highlight the ecological relevance and practical utility of AARL-PP and provide valuable guidance for selecting bioassessment tools tailored to tropical freshwater environments, supporting future water resource management and ecological monitoring in Thailand and similar regions.