Sulphur containing carboxy methyl ion imprinted polymers (S‐IIPs) were applied as an electrode modifier for the electrochemical detection of Hg(II). A bare glassy carbon electrode (GCE) was modified by electro‐polymerizing a layer of pyrrole and then drop coating with S‐IIPs. The bare GCE, GCE/polypyrrole (GCE/PPy), GCE/polyprrole/non‐ion imprinted polymers (GCE/PPy/NIPs) and the GCE/polypyrrole/sulphur ion imprinted polymers (GCE/PPy/S‐IIPs) electrodes were characterised with Fourier Transmission Infrared (FTIR) and electrochemical impendence spectroscopy (EIS). The square wave anodic stripping voltammetry (SWASV) optimised conditions for the GCE/PPy/S‐IIPs were: a pH of 3, deposition potential of −1.0 V, pre‐concentration time of 60 s and 0.1 M HCl supporting electrolyte. The developed ion imprinted polymer electrochemical sensor was applied in the detection of Hg(II) in water. A detection limit of 0.1 μg L−1 was calculated within a concentration range of 20–800 μg L−1. The sensor was selective in the presence of interfering ions and method was validated with inductively coupled plasma‐optical emission spectrometry (ICP‐OES) using real water and standard water samples.