The court ruled on Tuesday in favor of Swiss authorities, saying that while their refusal to exempt Muslim girls from the lessons interfered with their religious freedom, such interference is justified by the need to "protect" the children from social exclusion.
The court, based in the eastern French city of Strasbourg, did not, however, explain how the girls would suffer social exclusion by merely not attending swimming lesson amid numerous other school activities and learning experiences.
The court specifically insisted that the need to take part in swimming lessons at school especially applied to non-native pupils, ruling that school plays "a special role in the process of social integration, particularly where children of foreign origin were concerned."
Swimming lessons are "not just to learn to swim, but above all to take part in that activity with all the other pupils," it underlined without addressing the significance of engrained family values that are often faith-based and quite personal.
The case was brought by a Turkish-Swiss couple who argued that forcing their pre-pubescent daughters to take part in swimming classes with male students violated their faith.
All their appeals were rejected by Swiss courts, after which they took their case to Strasbourg. Tuesday's ruling, however, is not final. The couple has three months to appeal the decision.
The court favored Swiss authorities in arguing that they had tried to accommodate the beliefs of the Muslim family by allowing the girls to wear the full-body "burkini" swimsuit, something that many Muslims do not consider religiously legitimate in public.