Contamination of water systems with endocrine disrupting chemicals (EDCs) is becoming a major public health concern due to their toxicity and ubiquity. The intrusion of EDCs into water sources and drinking water has been associated with various adverse health effects on humans. However, there is no comprehensive overview of the occurrence of EDCs in Malaysia's water systems. This report aims to describe the occurrence of EDCs and their locations. Literature search was conducted electronically in two databases (PubMed and Scopus). A total of 41 peer-reviewed articles published between January 2000 and May 2021 were selected. Most of the articles dealt with pharmaceuticals (16), followed by pesticides (7), hormones (7), mixed compounds (7), and plasticisers (4). Most studies (40/41) were conducted in Peninsular Malaysia, with 60.9% in the central region and almost half (48.8%) in the Selangor State. Only one study was conducted in the northern region and East Malaysia. The Langat River, the Klang River, and the Selangor River were among the most frequently studied EDC-contaminated surface waters, while the Pahang River and the Skudai River had the highest concentrations of some of the listed compounds. Most of the risk assessments resulted in a hazard quotient (HQ) and a risk quotient (RQ) 1 in the Selangor River. An RQ > 1 for combined pharmaceuticals was found in Putrajaya tap water. Overall, this work provides a comprehensive overview of the occurrence of EDCs in Malaysia's water systems. The findings from this review can be used to mitigate risks and strengthen legislation and policies for safer drinking water.