The harvest and incubation of American Alligator (Alligator mississippiensis) eggs is an important component to the commercial alligator harvest industry in the southeastern United States. As a result, various methodologies have been used to monitor alligator populations including abundance counts, stress quantification, and nesting surveys. Past studies have dismissed the importance of egg shape in crocodilians, Squamates, and turtles and deemed egg shape in birds and other amniotes as similar, in relation to functionality. The complexity of crocodilian eggs has been examined, and both turtle and Squamate eggs have been regarded recently as physiologically more intricate than bird eggs. This study introduces a physiological approach to monitor alligator populations in freshwater and low salinity environments by quantifying egg shape in correlation with varying salinity. We introduce a fractional semilandmark-shape template method to quantify egg shape within a geometric morphometric framework. This approach is beneficial because it allows for the quantification of shape for curved structures, such as eggs, which lack homologous landmarks. The results from this study suggest that alligator egg shape is correlated with varying salinity levels, such that variation in alligator egg shape at low salinities changes in gradient-like fashion, whereas salinities high enough to be deemed stressful result in reversion back to a low salinity egg shape or desiccation. This study elucidates a correlation that can be implemented in management and breeding techniques and opens the door to in-depth physiological examination of the system.