Isotope hydrological studies to understand groundwater‐surface water interactions in tropical, high‐elevation catchments are limited. These interactions are important in controlling lake water residence time, aqueous biogeochemistry, and water availability for downstream communities and ecosystems. To better comprehend the complexity of spatio‐temporal variations in the aquifer‐lake domain in tropical volcanic regions, a multi‐tracer approach including water and inorganic carbon stable isotopes (δ2H, δ18O, δ13CDIC), hydrochemistry, and 222Rn was applied in Lake Hule, northern Costa Rica. Seasonal isotope mass balance calculations using lake, stream, precipitation, and groundwater compositions were supplemented with local hydrometeorological information. Evaporation to inflow ratios (E/I) revealed a small variability between the dry (December–April) and wet seasons (May–November), with relatively low evaporation losses, 2.9 ± 1.0 % and 3.2 ± 1.8 %, respectively. Bayesian end‐member analysis indicated that annual inputs from groundwater, precipitation, and runoff represented 61.3 ± 8.1%, 24.4 ± 8.4, and 14.3 ± 5.9% of total lake inflow, respectively. Temporal variations of δ13CDIC confirmed the key role volcanic carbonate buffering plays in this lake and indicated greater CO2 degassing from groundwater sources in the wet season. This tracer‐aided assessment in a volcanic lake maar of northern Costa Rica provides evidence of previously unknown groundwater‐surface water interactions and illustrates the application of isotopic tools for estimating water balances and seasonal variability of groundwater discharge into natural lakes across the volcanic front of Central America.