There are, of course, a lot of bathrooms all around Brookfield Zoo. I'll highlight a few of the best, based on general areas of the zoo. If you're seeking out the best bathrooms, the ones between Habitat Africa and the Great Bear wilderness are probably the best in the zoo that you don't need to pay extra for. From the African painted dogs, turn towards the Great Bear Wilderness and look for bathrooms ahead and to your right). Wild Encounters also has great bathrooms, and the Play Zoo bathrooms are nice, but both of those areas require an additional fee. If you're on the east side of the zoo, the best free bathrooms are just outside Wild Encounters at the Animal Ambassador building. The bathrooms by the South gate are also pretty good.
If you have young kids who don't always give you lots of warning, one big trouble spot is the northwest corner of the zoo (hoofed animals and Habitat Africa! The Forest in particular). Your best bet is probably to head towards the south end of Habitat Africa! and there are great bathrooms by the entrance to the Great Bear Wilderness. The other trouble spot is Tropic World, due to its size and lack of nearby public bathrooms. Head towards the Tropic World entrance (if you're in the third and final room of Tropic World, it's probably easiest to go out the exit and walk outside towards the entrance), you can then use the bathrooms by the South Gate entrance to the zoo.
Expand more information to get my recommendations for bathroom by area of the zoo.
Southwest corner: The Living Coast, Cafe del Sol, Feathers and Scales, Reptiles and Birds The bathrooms just outside Cafe del Sol are fine. If you're facing the entrance to Cafe del Sol, the entrance to go to the bathrooms is just to your right. There are some tight corners and there's not tons of space for strollers, but even double strollers can fit.
By the South Gate: Tropic World, The Swamp, Outside the Play Zoo The bathrooms by the South Gate are good, with lots of space for strollers once you get inside. Look just to the left of the South Gate (you'll need to go up a couple of steps or a small ramp). If you're in the Play Zoo, read the next category instead.
Inside the Play Zoo The bathrooms inside the play zoo are nice. They're narrow, but you can still fit a stroller inside. As you come into the Play Zoo, the bathroom is along the hallway ahead and to the right. There is also a family bathroom inside the Zoo at Home section in the back left of the Play Zoo.
Wild Encounters There's a great bathroom in Wild Encounters, straight ahead and to the left as you enter Wild Encounters, just after the goats.
Outside Wild Encounters If you don't want to go into Wild Encounters, but are nearby, use the great bathrooms in the Animal Ambassador building.
East side: Big Cats, Seven Seas (dolphins), Pinniped Point, BZ Red Hots The bathrooms below BZ Red Hots are fine. Facing BZ, take the ramp to the left of the building that goes down (from inside BZ Red Hots, you can also take the stairs down to the same bathrooms—if you're facing the counter where you order, walk to your left and around the corner to see the stairs). BZ Red Hots has bigger, but busier bathrooms which are very narrow to fit easily with a stroller when there are a lot of other people. The BZ Red Hots bathrooms also have two exits, so young kids can get confused and head out the wrong way. The family bathroom below BZ Red Hots can only be reached from outside.
By the North entrance: The Fragile Desert, Carousel, Australia The bathrooms by the North gate are pretty small and busy, but we've had to use them in a pinch. As you enter the zoo, they're by the line of shops to your left. You can also try the Discovery Center to see if it's open and bathrooms are available, these are much better but not always open: from the entrance, the newer building straight ahead and slightly to the right. If you're leaving (or haven't yet entered), instead use the bathroom by the parking lot which is very nice. If you're leaving the zoo, it's in a brick building to the left just as you get to the parking lot.
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