Taking a one-year-old to the swimming pool could increase their risk of infections that result in diarrhoea, research claims.
But it may not increase their risk of atopic diseases, as previously believed.
A study of 2,196 children undertaken by experts at the National Research Centre for Environment and Health found that babies who did not attend swimming pools in their first year had a much lower rate of infection, especially diarrhoea.
However, no connection was found between visiting the swimming pool and atopic disease, up to the age of six years.
Study author Dr Joachim Heinrich said: "In this way, the study shows that allowing babies to swim is possibly not as harmless with regard to infections as has been presumed till now."
Erich Wichmann, director of the GSF Institute of Epidemiology, said: "This is a first indication. Nevertheless, it requires other evidence to be able to achieve consequential results whether the water quality in German swimming pools protects sufficiently against infections in infants, and in particular, against gastro-intestinal infections."
The researchers add that a further trial of children who had not attended a swimming pool for ther first six years would be essential in drawing long-term conclusions about the impact swimming pools have on children's health.