Costa Rica is located on the Central American Isthmus, which receives moisture inputs directly from the Caribbean Sea and the Eastern Pacific Ocean. This location includes unique mountainous and lowland microclimates, but only limited knowledge exists about the impact of relief and regional atmospheric circulation patterns on precipitation origin, transport, and isotopic composition. Therefore, the main scope of this project is to identify the key drivers controlling stable isotope variations in daily-scale precipitation of Costa Rica. The monitoring sites comprise three strategic locations across Costa Rica: Heredia (Central Valley), Turrialba (Caribbean slope), and Caño Seco (South Pacific slope). Sporadic dry season rain is mostly related to isolated enriched events ranging from −5.8‰ to −0.9‰ δ18O. By mid-May, the Intertropical Convergence Zone reaches Costa Rica resulting in a notable depletion in isotope ratios (up to −18.5‰ δ18O). HYSPLIT air mass back trajectories indicate the strong influence on the origin and transport of precipitation of three main moisture transport mechanisms, the Caribbean Low Level Jet, the Colombian Low Level Jet, and localized convection events. Multiple linear regression models constructed based on Random Forests of surface meteorological information and atmospheric sounding profiles suggest that lifted condensation level and surface relative humidity are the main factors controlling isotopic variations. These findings diverge from the recognized ‘amount effect’ in monthly composite samples across the tropics. Understanding of stable isotope dynamics in tropical precipitation can be used to a) enhance groundwater modeling efforts in ungauged basins where scarcity of long-term monitoring data drastically limit current and future water resources management, b) improve the re-construction of paleoclimatic records in the Central American land bridge, c) calibrate and validate regional circulation models.