The pollution of heavy metal ions within the environment is a global problem. The rapid and precise removal of these contaminants can be aided by identifying and quantifying the composition of the sample. It is therefore crucial to develop effective portable analytical techniques to determine the levels of heavy metal contamination. Paper-based analytical devices (PADs) offer a low-cost method, making them an excellent platform for onsite environmental sensors. Here, we demonstrate how a PAD can be integrated into a multi-use nanopore platform. The PAD was functionalized with different recognition ligands, whose surface charge densities varied in the presence of an analyte. The surface of the PAD was placed in contact with a nanopore which exhibited ion current rectification (ICR). The extent of ICR was dependent upon the PAD’s surface charge and the presence of the analyte of interest, that is, the ICR phenomena was exaggerated or diminished indicating the presence of the metal ion in solution. We demonstrate the potential of PAD–ICR using a PAD functionalized with a peptide aptamer specific for nickel ions, allowing the detection of nickel(II) as low as 0.25 μM even in the presence of other metal ions. After any measurement, the nanopore surface can be wiped clean and reused. PAD–ICR can also be adapted as a multiplexed sensor. This is demonstrated using a PAD with three different DNA aptamers for simultaneous and specific detection of nickel, mercury, and lead ions.