The presence of emerging pollutants (EMPs) in aquatic environments poses serious threats to human and ecological health, yet their occurrence remains understudied in some countries, including the Kingdom of Eswatini. This research paper presents the first comprehensive investigation of EMPs in Eswatini's waters from wastewater treatment plants (WWTPs) with distinct treatment processes and surface water of the receiving rivers, utilizing a non-targeted screening approach with high-resolution mass spectrometry. It aimed to identify the occurrence and distribution patterns of EMPs while establishing baseline data to support subsequent quantitative research and remediation efforts. A total of 347 pollutants and their metabolites were identified, of which 181 were also detected in river samples. 64.6 % of all detected EMPs were pharmaceuticals: cardiovascular drugs, central nervous system drugs and antibiotics with 23.7 %, 21.3 % and 11.9 %, respectively, while pesticides accounted for 28.8 %. Highly toxic EMPs with acute/chronic toxicity <1 ppm, including nafronyl oxalate, lacidipine, dibutylone, phencyclidine, zolpidem, myclobutanil, mycophenolic acid, and multiple pesticides, were detected in over 50 % of river samples. Of the three WWTPs, Matsapha, which utilizes oxidative treatment processes showed notable effluent reductions in pharmaceuticals (42.0 %) and pesticides (34.4 %), while Ezulwini and Ngwenya WWTPs exhibited resurgences of up to 10.9 % and 33.1 %, respectively. This suggests treatment inefficiencies linked to the filtration/sedimentation and pond systems of the WWTPs. These findings highlight the persistent and occurrence of EMPs in Eswatini and underscore the need for targeted monitoring and improved waste management infrastructures.