Saltese Flats is in Water Resource Inventory Area (WRIA) 57, the Middle Spokane River, generally southeast of the City of Spokane Valley. Saltese Flats was a natural, shallow lake/wetland system, until around 1900, when much of the area was drained for agriculture.
Runoff from the watershed drains north off of Saltese Flats into Saltese Creek and eventually into Shelley Lake. Shelley Lake has no surface water outlet. Water in Shelley Lake infiltrates into the ground and recharges the Spokane Valley-Rathdrum Prairie (SVRP) aquifer.