Abstract Background Penguin interaction with gillnets has been extensively reported in the Atlantic and Pacific Oceans, and is considered a major conservation threat. Among penguin species, Magellanic penguins (Spheniscus magellanicus) are currently considered of great concern, particularly in Brazil, where they are highly susceptible to gillnet bycatch. Nevertheless, information about drowning-associated microscopic findings in penguins is limited. Results We describe the anatomopathological findings of 20 Magellanic penguins that drowned after getting entangled in a drift gillnet while wintering along the Brazilian shelf and washed ashore still enmeshed in Santa Catarina, Brazil. All 20 birds (19 juveniles and 1 adult; 18 females and 2 males) were in good body condition. Major gross findings were abrasion, bruising, and local erythema and edema of the wings, multiorgan congestion, jugular vein engorgement, pulmonary edema and hemorrhage, splenomegaly and hepatomegaly, fluid in the trachea, serous bloody fluid in the lungs, gastrointestinal parasites (nematodes, cestodes and trematodes), and debris in the stomach. The most common histopathological findings were cerebral and pulmonary congestion, pulmonary edema, splenic histiocytosis, lymphoid splenic hyperplasia, acute splenitis, extramedullary hepatic hematopoiesis, and parasitic enteritis. Although unspecific, the observed multiorgan congestion and pulmonary edema are consistent with previous reports of drowning in birds and may be indicative of this process. Conclusions Drowning may be a challenging diagnosis (e.g., carcass decomposition, predation), but must be considered as a differential in all beach-cast seabird postmortem examinations. To the authors’ knowledge this is the largest anatomopathological study based on microscopic examination in drowned penguins.