Concern over increasing numbers of double-crested cormorants (Phalacrocorax auritus) and their impacts on channel catfish (Ictalurus punctatus) aquaculture has resulted in increased need for quantitative information to develop and evaluate depredation management efforts. We evaluated aerial surveys in a stratified cluster sampling (SCS) design to estimate and monitor abundance of cormorants on catfish aquaculture ponds in the Yazoo River Basin of Mississippi, USA (hereafter Yazoo Basin). Twice monthly abundance estimates and coefficient of variation during winter averaged 8,128 (n = 29, SE = 1,233) and 33% (n = 29, SE = 0.02), respectively. Counts of cormorants on catfish aquaculture ponds between survey years were correlated (r = 0.87, n = 28). The correlation between diurnal counts of cormorants on ponds and cormorant night roost counts was 0.64 in 2000–2001 and 0.58 in 2003–2004 (n = 20 in both years). A priori estimates of sample size indicated an average increase in sampling effort of 39% during peak periods of cormorant use would be necessary to detect a ±15% change in cormorant abundance on aquaculture ponds at α = 0.05 and β = 0.80. The sampling design we used has the potential to be an effective tool for providing quantitative information on cormorant abundance on catfish aquaculture ponds in the Yazoo Basin. However, increased sampling effort would be necessary to obtain desired levels of precision. The SCS design we evaluated represents only one of many possible survey methods, and we recommend additional evaluation of this method and related survey methods.