We document the first use of fragile geologic features (FGFs) to set formal design earthquake motions for a major existing engineered structure. The safety evaluation earthquake (SEE) spectrum for the Clyde Dam, New Zealand (the mean 10,000 yr, ka, return period response spectrum) is developed in accordance with official guidelines and utilizes constraints provided by seven precariously balanced rocks (PBRs) located 2 km from the dam site and the local active Dunstan fault. The PBRs are located in the hanging wall of the fault. Deterministic PBR fragilities are estimated from field measurements of rock geometries and are the dynamic peak ground accelerations (PGAs) required for toppling. PBR fragility ages are modeled from cosmogenic isotope exposure dating techniques and are in the range of 24–66 ka. The fragility ages are consistent with the PBRs having survived at least two large Dunstan fault earthquakes. We develop a PGA‐based fragility distribution from all of the PBRs, which represents the cumulative toppling probability of a theoretical random PBR as a function of PGA. The fragility distribution is then used to eliminate logic‐tree branches that produce PGA hazard curves that would topple the random PBR with a greater than 95% probability (i.e., less than 5% survival probability) over a time period of 24 ka (youngest PBR fragility age). The mean 10 ka spectrum of the remaining hazard estimates is then recommended as the SEE spectrum for the dam site. This SEE spectrum has a PGA of , which is significantly reduced from the obtained for a preliminary version of the SEE spectrum. The reduction is due to the combined effects of the PBR constraints and a substantial update of the probabilistic seismic hazard model. The study serves as an important proof‐of‐concept for future applications of FGFs in engineering design.