Environmental flow (eflow) reference values play a key role in environmental water science and practice. In Mexico, eflow assessments are set by a norm in which the frequency of occurrence is the managing factor to integrate inter-annual and seasonal flow variability components into environmental water reserves. However, the frequency parameters have been used indistinctively between streamflow types. In this study, flow variability contributions in 40 rivers were evaluated based on hydrology, climate, and geography. Multivariate assessments were conducted based on a standardized contribution index for the river types grouping (principal components) and significant differences (one-way PERMANOVA). Eflow requirements for water allocation were calculated for different management objectives according to the frequency-of-occurrence baseline and an adjustment to reflect the differences between river types. Results reveal that there are significant differences in the flow variability between hydrological conditions and streamflow types (p-values < 0.05). The performance assessment reveals that the new frequency of occurrence delivers climate-smart reference values at least at an acceptable level (for 85–87% of the cases, r2 ≥ 0.8, slope ≤ 3.1), strengthening eflow assessments and implementations.