Retention, processing, and transport of solutes and particulates in stream corridors are influenced by the travel time of streamflow through stream channels, which varies dynamically with discharge. The effects of streamflow variability across sites and over time cannot be addressed by time-averaged models if parameters are based solely on the characteristics of mean streamflow. We develop methods to account for the effects of streamflow variability on travel time and compare our estimates to flow-weighted (“effective”) travel time at 100 streams in the southeastern United States. Velocity time series were generated for each stream from multiple-year (median 15.5 years), high-frequency (15 min interval) records of instantaneous streamflow and field measurements of velocity and inverted to produce time series of specific travel time [T/L]. The effective travel times for streams are 60–90% of the specific travel time of mean streamflow because a large fraction of the total streamflow volume is discharged during higher flows with higher velocities. We find that adjusting the specific travel time of mean streamflow at a site by a factor of 0.81 generally accounts for the effect of a skewed streamflow distribution, but at-site estimates of the coefficient of variation of streamflow are necessary to resolve differences in streamflow variability between streams or changes in variability over time. For example, the effective travel time of urban streams is less than the effective travel of forested streams in the southeastern United States as a result of increased streamflow variability in urban streams. Effective travel time accounts for both the variation in velocity with streamflow and the large fraction of streamflow discharged during high flows in most streams and provides time-averaged models with limited capability to account for effects of streamflow variability that otherwise they lack. This capability is needed for continental-scale modeling where streamflow variability is not uniform because of heterogeneous surficial geology, hydro-climatology, and vegetation and for applications where streamflow variability is not stationary as a response to climate change or hydrologic alteration.