Northern Map Turtles, Graptemys geographica, are a long-lived riverine species of conservation concern. We examined carapace morphology of Northern Map Turtles at Mount Union, a major turtle nesting area and former industrial site along the Juniata River in central Pennsylvania, USA. Among 535 reproductive adult female G. geographica, 29% exhibited abnormal shell shape, often in the form of an indentation in one or both sides of the carapace. Older females had a higher incidence of abnormalities than younger females. We quantified variation in shell shape, compared morphology among life history stages, and assessed thermal incubation environments of embryos to determine the magnitude and potential source of shell shape abnormalities. Geometric morphometric analysis showed significant differences among several carapace shape categories of adult turtles. No shell shape abnormalities were observed among 703 hatchlings collected from nests, and no shell shape abnormalities were observed among seven of those marked hatchlings that returned to Mount Union as 11- to 18-yr-old adult females to nest. Historically, most of the nesting substrate at Mount Union consisted of black coal tailings, which exposed developing embryos to high temperatures and potential chemical insults. The high incidence of abnormal carapace shapes of adult female Northern Map Turtles at Mount Union may reflect a delayed morphological response to chemical or thermal conditions encountered in the nesting substrate, direct exposure to contaminants in the Juniata River as subadults, or factors that affected turtles a generation ago but have since abated.