Heavy metal ions in polluted drinking water or in plants have attracted increasing public attention because of their extremely harmful effects on human beings and ecological equilibria. Therefore, identifying and assessing heavy metal pollution in different substrates are important. Traditional heavy metal ion detection methods, such as atomic absorption spectroscopy, electron capture devices, inductively coupled plasma optical emission spectroscopy, and mass spectrometry, which can be coupled to chromatographic techniques, require the use of large instruments. These techniques have high sensitivity to and specificity for different ions. However, the large, expensive instruments required by these techniques hinder the rapid, cost-effective detection of heavy metal ions in real applications. Thus, these methods are not suitable for real-time detection, and numerous studies have focused on making heavy metal ion detection more convenient and feasible. Accordingly, detection methods based on nucleic acid signal transmission have been developed to achieve rapid or real-time detection. In this chapter, the necessity of heavy metal ion detection methods, the advantages and drawbacks of traditional detection methods, and the latest nucleic acid-based detection methods are discussed. Moreover, the prospective applications of the different nucleic acid-based detection methods are presented.