Freshwater ecosystems are key to maintaining biological diversity and for human well-being. Despite their importance,
these ecosystems have suffered severe transformations due to anthropogenic activity. Here we present
the first priority assessment of freshwater ecosystems in Mexico at the national scale. Because species' compositional
and hydrological conditions vary widely across Mexico we divided the territory into seven distinct regions
in order to assign different conservation targets for biodiversity surrogates and to consider specific threats according
to their impact in each region. The total conservation area network identified is equal to 30% of the
country's continental surface, in which more than 94% of the biodiversity surrogates meet their established conservation
targets. The regions of the Tropical Pacific and Gulf of Mexico have the largest proportions of priority
sites, followed by the Central Highlands, which contains the largest number of irreplaceable sites. Tropical Pacific
and the Baja California Peninsula possess the largest proportion of sites with extreme importance for conservation.
Nationally, the percentage of priority sites under protection is 15.8%, of which 5.6% are sites of extreme importance,
4.2% are sites of high importance, and 6% are sites of medium importance for conservation. Our study
highlights the importance of conducting conservation prioritization assessments at higher spatial resolution
using information that is up to date and doing so in a collaborative way to strengthen decision making. This
analysis helps to bridge the research–implementation gap in conservation planning to improve the representation
of Mexico's freshwater biodiversity in conservation areas.