This paper investigates whether morphological variability of test and Aristotle’s lantern can be detected in sea urchins exposed to domestic pollution and whether this variability can be also related to tidal level and hydrodynamic features. The study was conducted on four sites along the French Basque coast. Each site is characterized by its geological layers’ orientation, regardless of its proximity to sewage outlets. Analyses on high-resolution pictures of jaws were performed and three parameters were retained: length, height and demipyramid dry mass. Five shape descriptors were consequently defined regarding the test and the jaws. Individuals with heavy test density associated with highly developed demipyramid regarding test diameter and height were preferentially observed in intertidal areas, remoteness from treatment plants and in south-oriented geological layers. High test hemispherical index and demipyramid elongation index were preferentially found far away from treatment plants. Results contribute to improving knowledge on pressure impact assessment and on state of the environment conservation in a defined area. It may also be useful to propose management measures on an appropriate scale for a species that is usually managed on a regional basis.