The stable isotope amount effect has often been invoked to explain patterns of isotopic composition of rainfall in the tropics. This paper describes a new approach, correlating the isotopic composition of precipitation with cloud height and atmospheric temperature using NEXRAD radar echo tops, which are a measure of the maximum altitude of rainfall within the clouds. The seasonal differences in echo top altitudes and their corresponding temperatures are correlated with the isotopic composition of rainfall. These results offer another factor to consider in interpretation of the seasonal variation in isotopic composition of tropical rainfall, which has previously been linked to amount or rainout effects and not to temperature effects. Rain and cloud water isotope collectors in the Luquillo Mountains in northeastern Puerto Rico were sampled monthly for three years and precipitation was analyzed for d18O and d2H. Precipitation enriched in 18O and 2H occurred during the winter dry season (approximately December–May) and was associated with a weather pattern of trade wind showers and frontal systems. During the summer rainy season (approximately June–November), precipitation was depleted in 18O and 2H and originated in low pressure systems and convection associated with waves embedded in the prevailing easterly airflow. Rain substantially depleted in 18O and 2H compared to the aforementioned weather patterns occurred during large low pressure systems. Weather analysis showed that 29% of rain input to the Luquillo Mountains was trade wind orographic rainfall, and 30% of rainfall could be attributed to easterly waves and low pressure systems. Isotopic signatures associated with these major climate patterns can be used to determine their influence on streamflow and groundwater recharge and to monitor possible effects of climate change on regional water resources.