The decision came after a woman was thrown out of an open-air pool for sunbathing topless and subsequently filed a complaint with the senate's ombudsperson's office for equal treatment.
The decision is expected to be welcomed by Germany's freikorperkultur, or free body culture.
Germany famously has a relaxed attitude to nudity, but the issue of whether and to what degree that is permissible at municipal swimming pools has plagued many local authorities.
The new rules apply to all visitors at Berlin's public pools and create legal certainty for staff.