The pollution of Nandu River, a tropical island river, is causing widespread concern due to the rapid development of agriculture and tourism. This study investigates the occurrence of contaminants of emerging concern (CECs) in the Nandu River at multiple scales, including basin-wide, seasonal, and media-specific variations. Samples were analyzed using a non-targeted screening (NTS) method involving solid phase extraction (SPE), liquid chromatography (LC), and high-resolution mass spectrometry (HRMS). A total of 257 CECs were identified in the flatwater samples. They mainly comprised primarily consisting of pesticides, pharmaceuticals, and industrial materials, indicating the simultaneous development of agriculture, farming, and tourism in river basin. The 75 CECs were quantified, and hierarchical clustering revealed the 20 most frequently detected CECs were strongly correlated with the pollution levels. The 75 CECs were further classified into distinct source clusters based on detection rates, providing insights into pollutant characteristics across different river sections. Comparisons between pollutants in various media showed minimal flux exchange, attributed to the pollutants' nature and the hydrological and water quality characteristics of island rivers. Seasonal variations in pollutant concentrations revealed that 63 CECs were present year-round in the Nandu River, with eight exhibiting high detection frequencies (>60 %) at all sites. Based on the 63 CECs detected year-round, a priority list of 36 control pollutants was developed using Agency's Aquatic Toxicity Profiles (ATP). This study provides valuable information to natural resource and public health agencies on Hainan Island and similar tropical islands, supporting ecosystem conservation, fisheries management, and human health risk assessments.