The data set presents the occurrence of 59 currently used pesticides (CUPs) and 33 pharmaceuticals and personal care products (PPCPs), from wetland areas, in Saudi Arabia, impacted by wastewater discharge. Wetlands are valuable ecosystems, but are very fragile and easily affected by anthropogenic pressure [1], [2], [3], [4], [5], [6]. The occurrence of organic contaminants provides understanding about their fate and possible risk for humans and environment. Up to our knowledge, this is the first report on the occurrence of the mentioned organic pollutants in shallow lakes in Saudi Arabia, and the first time these compounds are analyzed in wild flora. Samples of water, sediment, soil and plants were extracted via ultrasound assisted extraction (UAE) and solid phase extraction (SPE). The compounds determination was performed using ultra-high-performance liquid chromatography tandem mass spectrometry (HPLC-MS/MS). Interpretation and discussion of the present dataset can be found in the article entitled “Pharmaceuticals, pesticides, personal care products and microplastics contamination assessment of Al-Hassa irrigation network (Saudi Arabia) and its shallow lakes”[1].