Recently, molecular imprinted polymers (MIPs) were extensively used for separation and identification of specific molecules, replacing expensive and unstable biological receptors. Nonetheless, their application in electrochemical sensors has not been sufficiently explored. Here we report the use of a MIP as a specific receptor in a new highly sensitive tributyltin (TBT) electrochemical sensor. The sensor combines the specificity, pre-concentration capability and robustness of molecular imprinted polymer attached onto magnetic nanoparticles with the quantitative outputs of impedimetric measurements. The proposed device detects TBT in a concentration range of 5 pM to 5 µM with a low limit of detection (5.37 pM), which is lower than the one recommended for TBT in sea water by the US Environmental Protection Agency (EPA). We believe that this new electrochemical sensor can play an important role in the monitoring of the quality of sea and fresh waters worldwide.