Waterfowl surveys have been conducted on Cross Creeks National Wildlife Refuge from the early 1960's. Both ground count and aerial survey methods have been utilized. Earlier surveys were conducted each week throughout the entire year with most counts occurring from the ground. In 1991, the refuge changed the waterfowl survey timing to bi-weekly counts from September 1 - April 15 and stated that the preferred survey method would be aerial surveys. In 1998 the surveys were further modified, changing the timing to bi-weekly counts from mid-October through the first week of March.

Currently, the surveys are conducted infrequently beginning in mid-October and ending in early March. Some of these surveys are now conducted using a fixed-wing aircraft with one observer in addition to the pilot, the rest are done by ground counts. The weather and plane availability more often impacts when aerial surveys can be conducted.

Attempts are made using the same observer to survey all the waterfowl habitats within the refuge following the same route during each survey period. The data is recorded by waterfowl species. In addition to waterfowl, bald eagles, golden eagles, sandhill cranes, white pelicans, and common loons are recorded when observed.