Abstract Dry, ephemeral, desert wetlands are major sources of windblown sediment, as well as repositories for diapausing stages (propagules) of aquatic invertebrates. Zooplankton propagules are of the same size range as sand and dust grains. They can be deflated and transported in windstorm events. This study provides evidence that dust storms aid in dispersal of microinvertebrate propagules via anemochory (aeolian transport). We monitored 91 windstorms at six sites in the southwestern U.S.A. over a 17‐year period. The primary study site was located in El Paso, Texas in the northern Chihuahuan Desert. Additional samples were collected from the Southern High Plains region. Dust carried by these events was collected and rehydrated to hatch viable propagules transported with it. Using samples collected over a 6‐year period, 21 m above the ground, which included 59 storm events, we tested the hypothesis that transport of propagules is correlated with storm intensity by monitoring meteorological conditions such as storm duration, wind direction, wind speed, and particulate matter (PM10; fine dust concentration). An air quality monitoring site located adjacent to the dust samplers provided quantitative hourly measurements. Rehydration results from all events showed that ciliates were found in 92% of the samples, rotifers in 81%, branchiopods in 29%, ostracods in 4%, nematodes in 13%, gastrotrichs in 16%, and tardigrades in 3%. Overall, four bdelloid and 11 monogonont rotifer species were identified from rehydrated windblown dust samples. Principal component analysis indicated gastrotrichs, branchiopods, nematodes, tardigrades, and monogonont rotifer occurrence positively correlated with PM10 and dust event duration. Bdelloid rotifers were correlated with amount of sediment deposited. Non‐metric multidimensional scaling showed a significant relationship between PM10 and occurrence of some taxa. Zero‐inflated, general linear models with mixed‐effects indicated significant relationships with bdelloid and nematode transport and PM10. Thus, windstorms with high PM10 concentration and long duration are more likely to transport microinvertebrate diapausing stages in drylands.