Urban estuarine and coastal water receive several micropollutants through industrial and agricultural influxes. The bioaccumulation of these micropollutants in fish and their entry into the coastal population's food chain raises significant food safety concerns. Hence, a comprehensive analytical method was developed for ultra-trace level quantification of 345 micropollutants in fish. The optimized sample preparation method could extract compounds suitable for both GC–MS/MS and LC-MS/MS analysis simultaneously. The target list of contaminants included 278 agricultural pesticides and also 102 endocrine disruptors covering polyaromatic hydrocarbons, polychlorinated biphenyls, organochlorines, and endocrine-disrupting pesticides. The GC–MS/MS with large volume injection (LVI) technique, and LC-MS/MS operating in MRM mode, achieved an LOQ of <2.00 ng/g for most of the analytes. The extraction strategy involved tri-phase partitioning between water, acidified acetonitrile, and hexane, followed by salting out. Dispersive solid phase cleanup (dSPE) with C18, Z-Sep+, CaCl2, and MgSO4 was able to reduce the matrix influence, and the method achieved satisfactory recovery in the range of 70.0–120.0 % for all the target analytes. The repeatability and reproducibility relative standard deviation values of the measured analytes were <20.0 %, and the Horwitz ratio values were well below 2. The method was used to accurately measure the target micropollutants in fish from the Cochin estuary, the highly urbanized portion of the Vembanad Lake, and an important Ramsar site. At least one or more of the 41 different micropollutants were identified and quantified in about 90.7 % of the 108 samples analyzed. The importance of large-scale screening and trace-level quantification methods in environmental monitoring and risk assessment is underscored by the results. The risk assessment showed a moderate risk of exposure to the nearby coastal population through the food chain.