This document specifies methods and principles for detection of selected congeners of polychlorinated dibenzo-p-dioxins (PCDDs) and polychlorinated biphenyls (PCBs) in water and wastewater using a flow immunosensor. The flow immunosensor utilizes antibodies specific to 2,3,7,8-tetrachlorodibenzo-p-dioxin (2,3,7,8-TCDD) and 3,3’,4,4’,5-pentachlorobiphenyl (3,3’,4,4’,5-PeCB), which have the highest toxic equivalent factor (TEF) value among the congeners of each of PCDDs and PCBs. The method is applicable to timely monitoring of selected congeners of 2,3,7,8-TCDD and 3,3’,4,4’,5-PeCB in water and wastewater to prioritize those for subsequent confirmatory determination. This document specifies practical methods and procedures for sampling, extraction, clean-up, measurement in a flow immunosensor, data processing and validation of measurement results. The combined use of automated instruments for extraction, clean-up, and flow immunosensing can reduce time-consumption and labour-intensity, while providing reproducible precise data. This method can provide the lower limit of quantification (LOQ) for 2,3,7,8-TCDD and 3,3’,4,4’,5-PeCB of 28 pg/l and 152 pg/l, respectively at 20 % or less of coefficient variation (CV) depending on sampling, extraction, clean-up and measurement conditions.