The occurrence of endocrine-disrupting chemicals (EDCs) in the aquatic environment has brought increasing concern due to their potential adverse impacts on ecosystems and humans. These compounds are generally present in complex water matrices, such as surface waters at trace levels (ng L⁻¹) making their analysis difficult. In this work, an analytical method for the simultaneous determination of 13 EDCs, including 5 steroid estrogens, 1 progestogen, 1 androgen, and 6 endocrine-disrupting phenols in water, was developed using solid phase extraction (SPE), derivatization, and gas chromatography-mass spectrometry (GC-MS). The method was validated by spiking the 13 EDCs to the interest matrix. The recovery was in the range of 52–71% with an average of 62%. The limits of quantification were 1 and 5–10 ng L⁻¹ for phenolic compounds and hormones, respectively. The validated method was applied to assess the contamination level of the targeted EDCs in 15 sites collected from six rivers located at the cross-border area of Northern France and Belgium. The majority of the considered compounds were detected in the sampling sites and among them, bisphenol A (BPA) was found at the highest level which can be up to 286 ng L⁻¹. However, NP was the most frequently detected, followed by BPA and PG.