Lake Constance (southern Germany, western Austria and northern Switzerland). A week long cycling trip around the lake with a decent swim at least once a day in its clean, warm water. See Constance.
Slovenia's lakes and rivers. Four days of swimming in stunningly beautiful inland waterways in this little-explored jewel of eastern Europe. See Slovenia.
Italy's Lake Orta - fabulous scenery, history, art and cuisine - and yes and swimming. See Orta