Playas are ephemerally flooded wetlands found in hydrologically closed dryland catchments. Recent research showed how upland-catchment biophysical characteristics control the amount of organic carbon and nutrients that accumulates in playas from upland grasslands and shrublands. Here we further explored the role of allochthonous and autochthonous processes in fixing carbon and accruing soil nutrients in playas across a desert basin. We assessed whether playas contribute soil nutrient, organic-carbon stocks, and primary productivity rates in amounts disproportionately higher or lower than upland grasslands and shrublands. We found that playas had higher soil carbon and nutrient storage but no difference in mean annual primary production. Playas, on average, had similar primary productivity than upland systems, because they exhibited lower productivity during extremely wet years that offset the larger productivity during average or below average precipitation years. These results suggest that playas contain higher carbon and soil nutrient stocks because of runoff-mediated allochthonous inputs, rather than autochthonous sources, since long-term average productivity was similar to upland ecosystems. We also used the precipitation-aboveground net primary production (ANPP) relationships to accurately measure run-on in playas using differences between playa and upland grassland ANPP. The dependence of playa ANPP on surface-water inputs from upland catchments makes them susceptible to future changes in extreme precipitation events.