Because germination requirements of the exotic saltcedar (Tamarix ramosissima) and native cottonwood (Populus deltoides subsp. wislizenii) are similar, efforts to establish cottonwoods often result in concurrent establishment of saltcedars. We evaluated the success of fall flooding to reduce saltcedar seedling density in the Rio Grande floodplain of central New Mexico, USA. We also evaluated the effects of flooding on cottonwood seedlings. Six- to 8-week-old saltcedars and cottonwoods and 4-week-old saltcedars were completely submerged for a 30 day period from late August to late September. Effects of submergence were compared to a no submergence (control) treatment. Survival of 6- to 8-week-old saltcedar was 43.5 ± 5.61% in the submerged treatment and 66.25 ± 4.85% in the control. Survival of 4-week-old saltcedar was 2.0 ± 2.0% and 65.75 ± 8.74%, respectively, in submerged and control treatments. Cottonwood did not survive in the submergence treatment and 78.5 ± 10.4% in the control. Because of the high mortality of cottonwood in response to complete submergence, flooding saltcedar seedlings may not be desirable when submergence of cottonwood seedlings will also occur.