In the last years, progestins have raised special concerns for their documented negative effects on aquatic species, yet little is known about their environmental levels in surface waters and bioaccumulation in the trophic web. This study aimed to 1) adapt an extraction method for quantifying progestins in freeze-dried matrices, 2) validate the analytical procedure for three matrices: bivalve, polychaete, and crustacean, and 3) characterize levels of the four most prescribed synthetic progestins in key species across three Portuguese estuaries. Through the validated method, progestins were only quantifiable for the crustacean. Values were generally low, peaking with drospirenone values in Ria de Aveiro (1.33 ± 0.26 ng/g ww) and Tagus estuary (1.42 ± 0.55 ng/g ww), while Ria Formosa exhibited the lowest progestin concentrations (< 1 ng/g ww). This study enabled the development of a precise extraction and analytical method for quantifying steroid hormones in three distinct biological matrices.