In the wake of rapid advancements in the pharmaceutical, food, and agricultural industries, the environment faces an increasing influx of diverse compounds, both intentionally and unintentionally released. These compounds fall into two categories: persistent and emerging pollutants. Persistent pollutants, characterized by their resistance to degradation and potential to accumulate in the environment, pose serious ecological threats. The Water Framework Directive (WFD) plays a pivotal role in monitoring and regulating these substances. This review discusses various contemporary analytical approaches to determine problematic substances, including benzo(a)pyrene, cypermethrin, dichlorvos, heptachlor, and heptachlor epoxide, aligning with the priorities outlined in the 2013 WFD classification. This review focuses on diverse water sampling methods, sample preparation techniques, and analytical methods, encompassing chromatographic, spectroscopic, and electrochemical approaches, with the primary goal of achieving the requirement laid on analytical methods used for the determination of maximum allowable concentrations defined in the WFD. Chromatographic methods, utilizing diverse mass spectrometers, have achieved detection limits as low as 10−6 μg/L, while modern electroanalytical techniques reach levels as low as 10−13 μg/L, reflecting an ongoing collective effort to enhance monitoring and safeguard the health of aquatic ecosystems. From sampling methods, large-volume sampling and passive sampling devices have been shown to be a cost-effective and modern solution, addressing limitations in traditional sampling methods, even if both of them face important pros and cons in terms of quantitative analysis.