Short answer: "them" refers to "the great waters." This same language is used throughout scriptures from YHWH because YHWH created them.
- The first clue is in Ezekiel 32:2-3. I'm quoting from KJV.
"Son of Man, take up a lamentation for Pharaoh, king of Egypt, and say unto him, Thou art like a young lion of the nations and thou art as a whale in the seas: and thou camest forth with thy rivers and troubledst the waters with thy feet, and fouledst their rivers. Thus saith the Lord God, I will therefore spreadeth my net over thee with a company of many people and they shall bring thee up in my net." (v 2-3)
Pharaoh and his army fouled the waters (against Israel) and they will be captured in those waters.
- The second clue is in a comparison of other translations.
"Also I will destroy all its animals from beside its great waters; the foot of man shall muddy them no more, nor shall the hooves of animals muddy them."
"I will slaughter all its cattle that are beside many waters. No human foot will churn them again, and no cattle hooves will disturb them."
"I will destroy all its cattle beside the plentiful waters; and no human foot will disturb the waters again, nor will the hooves of cattle disturb them."
- Taking the story into context...
"Then I will leave thee upon the land, I will cast thee forth upon the open field, and will cause all the fowls of the heaven to remain upon thee, and I will fill the beasts of the whole earth with thee." (v 4)
The waters have already destroyed the Pharaoh and his army and he in turn, has fouled up the waters. The "net" (a symbol) will be cast on the earth, where birds and beasts will eat their flesh.
"And I will lay thy flesh upon the mountains and fill the valleys with thy height." (v 5)
The flesh of the Pharaoh and his army will be scattered on the earth.
"I will also water with thy blood the land wherein thou swimmest, even to the mountains; and the rivers shall be full of thee." (v 6)
The Pharaoh's blood will run down the mountains, into the rivers, which will fill with blood.
"And when I shall put thee out, I will cover the heaven, and make the stars thereof dark; I will cover the sun with a cloud, and the moon shall not give her light. All the bright lights of heaven will I make dark over thee, and set darkness upon thy land." (v 7-8)
The Pharaoh and his army will decompose under darkness.
"I will also vex the hearts of many people when I shall bring thy destruction among the nations, into the countries which thou hast not known. Yea, I will make many people amazed at thee, and their kings shall be horribly afraid for thee, when I shall brandish my sword before them; and they shall tremble at every moment, every man for his own life, in the day of thy fall." (v 10)
People will fear the Pharaoh and his army and be afraid for them, when they are destroyed.
"For thus saith the Lord God; the sword of the king of Babylon will come upon thee." (v 11)
Pharaoh will be defeated by the king of Babylon.
"By the swords of the mighty will I cause the multitude to fall, the terrible of the nations, all of them: and they shall spoil the pomp of Egypt, and all the multitude thereof shall be destroyed." (v 12)
YHWH has laid out specifically what will happen (2-11), then refers to it in one simple sentence.
This is a chapter about the Pharaoh and how he has hurt the Israelites and how he'll be destroyed. "The great waters" were a tool to destroy Pharaoh and his army but those waters wound up being "troubled" (v 13) in the process.