The detection of hormones, pharmaceutical and personal care products (PPCPs), in aqueous complex media as water bodies is an urgent and mandatory matter because of its harmful impact on the environment. This work presents a sensor device which is able to detect trace of the synthetic hormone 17α-ethinylestradiol (EE2), in a range of concentration of 10-15 to 10-9 M in both mineral and tap waters. These types of water were studied due to their different degrees of complexity, which allow to attain a better understanding of EE2’s behavior and response in different media. The sensor body consists of solid supports having interdigitated electrodes without and with a thin film deposited on it, and device response is evaluated through impedance spectroscopy. The thin films were prepared by the layer-by-layer technique from aqueous solutions of polyethylenimine (PEI) and poly(sodium 4-styrenesulfonate) (PSS) polyelectrolytes. Results demonstrated that it is possible to discriminate clearly the different waters used and to detect EE2, obtained from the second principal component (PC2) as a result of the application of principal component analysis method, with a sensitivity of -0.072 ± 0.009 and -0.44 ± 0.03 per decade of concentration, for mineral and tap water, respectively. Detection limits values were found to be of 8.6 fM (2.6 pg/L) and of 7.5 fM (22.2 pg/L) for TW and MW, respectively and are lower than the ones found in literature. Moreover, the achieved constant proportionality between the PC2 values for each EE2 concentration reveals that one can use this methodology to quantify EE2 concentration in unknown aqueous complex matrices.