The first thing to make sure you've set up correctly is that your animal keepers have fast access between your store room, where they collect food for your animals, to the enclosure itself. The less time your animal keepers have to spend walking, the more time they have to carry out their duties in a day.

Subways are a huge help here - you can have your store room anywhere in your zoo, as long as you've got a subway next to it, and subway access close to all of your enclosures.

Here, I have a subway directly opposite the store room with only a few tiles walking distance:


And then I have a subway near each enclosure or cluster of enclosures, with the gate to the enclosure placed close to the subway exit for optimal Keeper access:

If your animal keepers can't get to the poop, they can't clean it :D

One of the most fun aspects of the game is decorating your animal enclosures, but be careful not to place structures in a way that blocks off access.

You can check your collision map from the top right menu - make sure that your objects aren't placed so close together that they're blocking movement through them;


The red squares represent squares that can't be walked on, and red corners touching means your keepers won't be able to move between these objects. In the screenshot above I have some objects in the enclosure that are touching, but there's a clear path around the left of them, so the animal keeper can still walk around them.

In this image, the keepers can't get to the poop because it's closed on all four sides by the trampolines and water; it looks like there's a space but the collision boxes for the trampolines are a bit bigger than the actual trampoline, so it's important to check :D (Thanks to Tuga on Discord for allowing me to use this image of their bunny poop shame XD)