Fluridone is widely used as a herbicide for controlling invasive aquatic plants such as hydrilla in surface water bodies. When applied on surface waters fluridone can attach to bed sediment, requiring rigorous extraction methods prior to analysis. Currently, very limited information exists in terms of fluridone residue detection in delta sediment. In this study, we researched fluridone detection in both water and sediment. To extract fluridone from sediment, here we have tested two extraction methods: (1) a rotavapor method (RM); and (2) a quick, easy, cheap, effective, rugged and safe (QuEChERS) method (QM). The extraction results of RM were compared with those of QM. To quantify fluridone concentrations in extracts, a high-performance liquid chromatography (HPLC)-UV detector was used. HPLC separation was achieved using an Allure C18 5 µm 150 × 4.6 mm column with a mobile phase composed of acetonitrile and water (60:40, v/v). The UV detector was operated at 237 nm. The method was tested and validated using a series of water and sediment samples taken from Sacramento-San Joaquin Delta in California. The average recovery of fluridone was 73% and 78% using RM and QM respectively. The proposed method can be used for testing fluridone in water and sediment samples.