The mean transit time (MTT) of water is an essential descriptor of streamflow generation and catchment water storage. Research on how MTTs fluctuate over time and the variables influencing such variation is limited. In this study, bi-weekly stable isotopic data in precipitation and streamflow were used, together with daily records of hydrometeorological information, to investigate the temporal variability of streamflow MTTs. The data were collected over 8 years in a nested system of 8 tropical alpine catchments in the Zhurucay Ecohydrological Observatory in southern Ecuador (3,450 to 3,900 m a.s.l.). The temporal variability of streamflow MTTs was estimated using yearly periods and a 1-month moving window (i.e., 81 yearly calculated MTTs per catchment). The factors controlling the temporal variability of MTTs were identified using simple and multiple linear regression models with hydrometeorological parameters as explanatory variables. Results reveal that streamflow MTTs in all catchments were short (<1 year) and varied little among catchments (191.30 ± 47.10 days). A combination of hydrometeorological variables (i.e., precipitation, streamflow, and runoff coefficient) over antecedent periods up to 1 year was found to control MTT temporal variability. Overall, these findings point to the prevalence of low temporal variability of hydrological conditions in the investigated catchments. Our study is key to provide insights into the factors controlling the temporal variability of streamflow MTT in tropical catchments, overcoming data limitations of past investigations and with significant implications for improved water supply management.