To evaluate bird damage to lotus roots, Nelumbo nucifera Gaertn. (Proteales: Nelumbonaceae), we collected 170 damaged roots from eight flooded lotus fields around Lake Kasumigaura. There were 258 samples of feeding marks, so-called “duck damage,” and 41 samples of disease damage. The shapes of the feeding marks were categorized into seven types: touch, sharp-peck, shallow-scoop, deep-scoop, boat, cross-section, and eat-up. We experimentally placed the lotus roots in a post-harvest lotus field and confirmed six types, excluding shallow-scoop, from our observation of the leftovers eaten by Eurasian Coots, Fulica atra L. (Gruiformes: Rallidae), and Mallards, Anas platyrhynchos L. (Anseriformes: Anatidae). To compare the shape of the damage with bill size, we tested on crows in captivity. While scars caused by numerous pecks impeded the identification of the suspect species, the width of a single sharp-peck by Eurasian Coots or Large-billed Crows, Corvus macrorhynchos Wagler (Passeriformes: Corvidae), matched their bill width. In the mud of the lotus fields, the color around the feeding marks changed to purple-black after a couple of days, but the shapes did not change and differed from disease damage. Therefore, damaged roots claimed as “duck damage” were caused by ducks and coots’ feeding, and a single sharp-peck can be identified as being caused by coots’ pecking action.