The anomalously low oxygen isotope ratio (δ18O values) of tropical cyclone rainfall can transfer proxy information about past tropical cyclone activity to stalagmite oxygen isotope records. Isotopically distinct stormwater reaches the growing crystal surface as a coherent slug, or after attenuation by mixing with isotopically normal vadose groundwaters. A high-resolution micromilled stalagmite stable isotope record from Belize shows that residual tropical cyclone water from Hurricane Mitch masked the oxygen isotope record of a major El Niño event. On decadal time scales, measured δ18O values are affected by changes in local tropical cyclone frequency. Despite the tropical cyclone masking effect, the structure of the “missing” El Niño event is preserved in the ATM-7 carbon isotope ratios (δ13C values). In tropical cyclone-prone regions, the fidelity of stalagmite oxygen isotope proxy data to recording background climate signals is modulated by temporal variations in local tropical cyclone rainfall, and the sensitivity of individual stalagmites to tropical cyclone masking varies with hydrology. Speleothem δ13C values, unaffected by tropical cyclones, can preserve the underlying structure of climatic variability. For low-latitude speleothems with C–O isotope covariance, intervals in which the δ18O values are significantly lower than δ13C values predict may indicate periods when local tropical cyclone masking of isotope-derived precipitation records is enhanced by greater infiltration of tropical cyclone rain. The temporal structure in stalagmite C–O isotope covariance has paleoenvironmental meaning that may be revealed by exploring factors associated with independent behavior in each isotope ratio, respectively. Tropical cyclone masking presents new challenges to paleoclimatology and a source of hypotheses for paleotempestology.