The interaction between vegetation and the atmosphere is highly complex in fog affected ecosystems like Tropical Montane Cloud Forests (TMCFs). Despite acknowledging fog effects on the canopy's water balance, quantifying their influence remains challenging. While the reduction in potential evaporation that is caused by fog presence, is largely independent of land cover, fog interception itself strongly depends on the land-cover's vegetation characteristics. A better understanding of how these two fog related processes affect the water balance is highly relevant under current land-use and climate-change pressures. In this study we evaluate the different fog effects on TMCFs’ canopy interception combining model simulations and high temporal resolution (10 min) observations that were collected in different TMCF regeneration stages: early succession, secondary and old-growth TMCFs. We also analyse the difficulties in closing catchment water balances caused by limitations on the interpretation of throughfall data to properly represent these fog effects. Results show that different fog frequencies along elevation affect potential evaporation. The higher elevation old-growth TMCFs have a lower simulated evaporation and a lower dry canopy frequency than the low elevation secondary and early succession forests. Furthermore, we show that fog water inputs during fog-only events, even though higher at the higher elevation, are irrelevant as water inputs (from 0.8% to 1.6% of measured rainfall), but fog's contribution to through-fall during foggy rainfall events can be more relevant (from 5.8%–12.8% of measured rainfall). Additional to the fog trends along the elevation, we also uncover variable fog-vegetation interactions controlled by differences in canopy water storages as a function of forest cover. Each evaluated process has associated uncertainties, which together cumulatively explain why closing a water budget in TMCF catchments is limited by data collection methods that probably do not capture all relevant fog effects. In addition, this study also indicates that the temporal resolution of measured rainfall and through-fall and compensating effects of canopy parameters that are estimated by the commonly used Rutter canopy-rainfall interception model, pose an additional challenge to understand and quantify fog effects in the water budgets of TMCFs.