High pressure liquid chromatography (HPLC) with amperometric detection was used to quantify estrogenic compounds in water samples. The main goal was to compare the detection figures of merit for boron‐doped diamond thin‐film (BDD) and nitrogen‐incorporated tetrahedral amorphous carbon (ta‐C : N) thin‐film electrodes. The target analytes were estrone, estradiol, and estriol. The BDD and ta‐C : N electrodes were investigated because of their excellent properties, which include a wide potential window, low background current, microstructural stability at high potentials, low limits of detection, weak molecular adsorption, fouling resistance and response reproducibility. ta‐C : N electrodes have not yet been investigated extensively in electroanalysis and are receiving increasing interest because they exhibit many of the excellent electrochemical properties of BDD electrodes and they can be deposited at room temperature by physical vapor deposition. The results reveal as low or lower background current and noise for the ta‐C : N electrode, as compared to the BDD electrode, and comparable or superior analytical detection figures of merit for all three emerging pollutants. The linear dynamic range for both electrodes was from 0.2 to 100 μmol L−1 for estriol, and 0.4 to 100 μmol L−1 for estradiol and estrone, and the sensitivity ranged from 9.1 to 11.2 mA mol L−1. For all three analytes, the limit of detection (S/N=3) ranged from 0.16–0.35 μmol L−1 (45‐95 ppb) for BDD and 0.20–0.34 μmol L−1 (58‐95 ppb) for ta‐C : N.