Stable isotope variations are extremely useful for flow partitioning within the hydrologic cycle but remain poorly understood throughout the tropics, particularly in watersheds with rapidly infiltrating soils, such as Andisols in Central America. This study examines the fluctuations of stable isotope ratios (d18O and d2H) in the hydrologic components of a tropical coffee agroforestry watershed (~1 km2) with Andisol soils in Costa Rica. Samples were collected in precipitation, groundwater, springs, and stream water over 2 years. The local meteoric water line for the study site was d2H = 8.5 d18O + 18.02 (r2 = 0.97, n = 198). The isotope ratios in precipitation exhibited an enriched trend during the dry season and a notable depletion at the beginning of the wet season. The d18O compositions in groundwater (average = -6.4‰, s = 0.7) and stream water (average = -6.7‰, s = 0.6) were relatively stable over time, and both components exhibited more enriched values in 2013, which was the drier year. No strong correlation was observed between the isotope ratios and the precipitation amount at the event or daily time-step, but a correlation was observed on a monthly scale. Stream water and base flow hydrograph separations based on isotope end-member estimations showed that pre-event water originating from base flow was prevalent. However, isotope data indicate that event water originating from springs appears to have been the primary driver of initial rises in stream flow and peak flows. These results indicate that isotope sampling improves the understanding of water balance components, even in a tropical humid location, where significant variations in rainfall challenge current modelling efforts. Further research using fine-scale hydrometric and isotopic data would enhance understanding the processes driving spring flow generation in watersheds.