Halogenated polycyclic aromatic hydrocarbons (HPAHs) including chlorinated (ClPAHs) and brominated (BrPAHs) variants, are emerging contaminants that are considered the next-generation candidates of persistent organic pollutants. Since there was a significant gap exists in understanding of partitioning dynamics of HPAHs between the particulate phase (PP) and dissolved phase (DP) considering many congeners, this study analyzed 75 congeners of parent PAHs and HPAHs (p/HPAHs) in the samples collected from 27 sites from 20 water bodies in Sri Lanka. The results revealed that the mean of the total concentrations of PAHs, ClPAHs, and BrPAHs in the aqueous phase (PP + DP) were 55.79, 1.89, and 0.49 ng/L, respectively. Partition coefficients of HPAHs increased with molecular weight, and pyrene and its halogenated derivatives dominated both phases. A predominance of HPAHs in the DP suggested that their distribution was more influenced by source characteristics than by phase partitioning processes. Most p/HPAHs originated from mixed petroleum and combustion sources, with additional input from decaying contaminated biota. The risk quotients determined via the acute and chronic ecological risk assessment indicated many waterbodies had medium to high risks to fish and daphnids, whereas the consumption of well water for drinking purposes did not pose a risk to humans. This study provides the first comprehensive phase-specific evaluation of HPAHs in a tropical aquatic environment and calls for targeted monitoring strategies, effective management plans, and public awareness to mitigate future contamination.