The surface properties of carbon film electrode sensors covered by coating with Nafion polymer film, before and after electrochemical analysis of sub-micromolar traces of lead and cadmium ions, were investigated. These protective polymer films are applied to the electrode surfaces to prevent the irreversible adsorption of chemical species, such as proteins and surfactants present in natural media, which leads to a decrease in response. Electrochemical impedance spectroscopy and voltammetric techniques were used for characterisation. The effect of non-ionic surfactant molecules in solution on the behaviour of the polymer-coated electrode was also investigated. It is shown that permanent changes to the structure and morphology of the Nafion film and of the carbon-Nafion interface occur after deposition of the trace metal ions, an effect which is lessened in the presence of surfactant.