Nafion is widely used as a filtering membrane in electroanalytical applications to improve selectivity towards cations. However, the role of the thickness of Nafion on its electroanalytical performance is poorly understood. Furthermore, Nafion is often modified with additional elements without characterizing their influence on Nafion's filtering properties. To understand in-depth these uncharacterized effects on Nafion, we approach these issues systematically by studying first (i) the role of Nafion film thickness on top of a well characterized tetrahedral amorphous carbon electrode and second (ii) introducing nanodiamonds into the same Nafion films with different thicknesses. With careful electrochemical and structural analyses, we show that already ultrathin Nafion film significantly reduces limiting currents of anionic species IrCl63-/4- and uric acid. With a thicker film (similar to 3.6 mu m) the selective nature of Nafion is demonstrated as anionic species are completely filtered and enrichment of cationic species Ru(NH3)(6)(2+/3+) is achieved. However, diffusion within the film controls the overall kinetics of the cation reactions and the electrochemical performance of Nafion is heavily dependent on the width of the potential window used. In addition, we show that modifying Nafion with nanodiamonds increases permeability of both cationic and anionic species. Hence, Nafion's ability for selective detection of cations is greatly reduced. Interestingly, chemical effects were also observed between nanodiamonds and an inner sphere redox probe uric acid. Thus, additional elements in Nafion do not only affect the physical structure of the film, but may produce chemical changes as well. Based on the results presented here, we emphasize the importance of an in-depth investigation to understand the case specific effects of modified Nafion films to guarantee the reliability of the sensor devices in the final application.