The Yazoo River Basin of Mississippi, USA, supports the largest concentration of hectares devoted to channel catfish, Ictalurus punctatus, aquaculture production in North America. The Yazoo Basin also supports large numbers of resident, wintering and migrating fish-eating birds, with the Double-crested Cormorant, Phalacrocorax auritus, implicated as the most serious depredating species. We used data from aerial surveys of numbers and distribution of cormorants in the Yazoo Basin and on commercial catfish ponds during winters (November–April) 2000–2001 and 2003–2004 to refine estimates of regional economic losses due to cormorant depredation. In both periods, the greatest monthly estimates of cormorant foraging occurred from 1 January to 31 March. Losses in terms of biomass, number, and dollar value were greater for foodfish ponds than fingerling ponds. Monthly weighted estimates of catfish consumed were 1775.3 and 1346.6 m.t. over winters 2000–2001 and 2003–2004, respectively. Total estimated losses for foodfish and fingerling ponds in 2000–2001 were $11.56 and $0.48 million, respectively, and in 2003–2004 were $5.22 and $0.40 million, respectively. Maximum dollar loss occurred during March in 2000–2001 and during February in 2003–2004. In this study, the volatility in variable production costs and nominal sales price, and distribution of cormorants on pond types and regionally were key factors in resulting economic loss estimates.