Aim: This study aimed to determine the pesticide pollution and prevalence of protozoa in anurans from lowland and highland golf courses in Malaysia and to observe the relationship between environmental factors (water quality index and pollutants) and the presence of protozoa in anurans. Methodology: Water quality index and pesticide levels (metsulfuron methyl) were measured at three locations, i.e. Jeriau river, Fraser's hill golf course in Pahang, and UKM Danau golf club in Selangor. Microscopy techniques were used to identify and examine the prevalence of protozoa and haemoparasites in anuran organs (stomach, kidney, liver, intestine, rectum, and blood). Results: A total of 140 anurans were collected from the study areas. Jeriau river had the highest water quality compared to Fraser's hill golf course and UKM Danau golf club. Metsulfuron methyl concentrations at all three locations were under permissible level (0.001–0.01 mg l-1). Approximately, 30% of the anurans were infected with ≥ 1 protozoa, of which 22.14% were from phylum Opalinata and 10.71% were from phylum Ciliophora (Nyctotherus cordiformis). Approximately 44.44% of the anurans were infected with ≥ 1 groups of haemoparasites, which included Trypanosoma, Haemogregarina, Lankesterella, Aegyptianella and Microfilaria. Interpretation: No significant relationship was found between the environmental parameters and the abundance of protozoa and haemoparasites in anurans from three locations, indicating that the prevalence of protozoa and haemoparasites in anurans is not influenced by environmental factors.