Uranium is an essential raw material in nuclear energy generation; however, its use raises concerns about the possibility of severe damage to human health and the natural environment. In this work, we report an ultrasensitive uranyl ion (UO2(2+)) detection method in natural water that uses a plasmonic nanowire interstice (PNI) sensor combined with a DNAzyme-cleaved reaction. UO2(2+) induces the cleavage of DNAzymes into enzyme strands and released strands, which include Raman-active molecules. A PNI sensor can capture the released strands, providing strong surface-enhanced Raman scattering signal. The combination of a PNI sensor and a DNAzyme-cleaved reaction significantly improves the UO2(2+) detection performance, resulting in a detection limit of 1 pM and high selectivity. More importantly, the PNI sensor operates perfectly, even in UO2(2+)-contaminated natural water samples. This suggests the potential usefulness of a PNI sensor in practical UO2(2+)-sensing applications. We anticipate that diverse toxic metal ions can be detected by applying various ion-specific DNA-based ligands to PNI sensors.