Monitoring organic pesticides in surface water using grab water sampling method is ineffective in most cases due to pesticides’ irregular emission and low solubility in water. To address the problem in water sampling method, this study used passive samplers (PS) composed of silicon rubber sheets (SR) and speedisk (SD). SR and SD were used respectively to measure hydrophobic and hydrophilic organic pesticides. These were submerged in river water uninterruptedly for 34 days. Pesticides in PS were extracted and analysed by sensitive analytical instruments HPLC, GC-MS MS and LC-MS MS. Pesticide assessment were conducted in two river systems in Cagayan de Oro River Basin, Philippines where agricultural run-off are unintentionally and continuously disposed from medium to huge plantations. The samplers were able to measure 105 emerging organic pollutants of which, 56 were organic pesticides and 22 organochlorine pesticides (OCP). Out of 56 pesticides, 11 were measured beyond the applied threshold level of 10ng/L. These were boscalid, carbendazim, dimethomorph, metalaxyl, propiconazole, pyrimethanil, diuron, monuron, simazine, dichlorvos and phenamiphos. The 22 OCP, despite being banned or restricted for almost two decades, were measured in ultra-traces of ng-pg/L. The data obtained in this study can be used to establish a baseline background level which is currently absent in most river systems in the Philippines. It is recommended that further study will be conducted using software PBPK or NORMTOX to assess health impacts and implications of the measured pesticides on the communities that are dependent, and continuously exposed to these constituents by these river waters.