We explored the feasibility of sampling young-of-year (yoy) Gulf sturgeon (Acipenser oxyrinchus desotoi) in the Apalachicola River, Florida, using modified balloon trawls during January and June 2009. Three yoy sturgeon (57 - 120 mm TL) were captured during June 2009 in the lower reaches of the river system. Initially, this method of assessment is labor intensive and may require more than 25 river kilometers (rkm) of trawling per capture. While this gear type has been remarkably efficient for sampling yoy Scaphirhynchus (i.e., pallid and shovelnose sturgeon) in the Mississippi River system, the depressed population size (ranging from a few hundred to perhaps 1,000 individuals) encountered in the Apalachicola River could make assessment of yoy Gulf sturgeon problematic.