It is not known because the relevant part of the Sumerian version of the myth is missing, but in later versions the cause is the god Enlil.
From an article in Livius.org: The Great Flood: Sumerian version.
The story survives on a cuneiform tablet from the seventeenth century
BCE, of which only the lower third survives. However, this is
sufficient to establish that the pattern described above was already
present. However, there are small differences. The Eridu Genesis must
have begun with the Creation of Man, but continues with the
establishment of kingship and a list of cities. Then comes the list of
antediluvian rulers, which confirms the pattern again, and the supreme
god Enlil's decision to destroy mankind. The reason was recorded on a
missing part of the text, but may have been the noise men created, as
it is in the later, Babylonian texts.
From the Wikipedia article about Enlil:
Enlil plays a vital role in the Sumerian creation myth; he separates
An (heaven) from Ki (earth), thus making the world habitable for
humans. In the Sumerian Flood myth, Enlil rewards Ziusudra with
immortality for having survived the flood and, in the Babylonian flood
myth, Enlil is the cause of the flood himself, having sent the flood
to exterminate the human race, who made too much noise and prevented
him from sleeping.
In the same Wikipedia article, under the Flood Myth section:
In the Sumerian version of the flood story, the causes of the flood are unclear because the portion of the tablet recording the beginning
of the story has been destroyed. Somehow, a mortal known as Ziusudra
manages to survive the flood, likely through the help of the god Enki.
The tablet begins in the middle of the description of the flood. The
flood lasts for seven days and seven nights before it subsides. Then,
Utu, the god of the Sun, emerges. Ziusudra opens a window in the side
of the boat and falls down prostrate before the god. Next, he
sacrifices an ox and a sheep in honor of Utu. At this point, the text
breaks off again. When it picks back up, Enlil and An are in the midst
of declaring Ziusudra immortal as an honor for having managed to
survive the flood. The remaining portion of the tablet after this
point is destroyed.
In the later Akkadian version of the flood story, recorded in the Epic of Gilgamesh, Enlil actually causes the flood, seeking to
annihilate every living thing on earth because the humans, who are
vastly overpopulated, make too much noise and prevent him from
sleeping. In this version of the story, the hero is Utnapishtim, who
is warned ahead of time by Ea, the Babylonian equivalent of Enki, that
the flood is coming. The flood lasts for seven days; when it ends,
Ishtar, who had mourned the destruction of humanity, promises
Utnapishtim that Enlil will never cause a flood again. When Enlil sees
that Utnapishtim and his family have survived, he is outraged, but his
son Ninurta speaks up in favor of humanity, arguing that, instead of
causing floods, Enlil should simply ensure that humans never become
overpopulated by reducing their numbers using wild animals and
famines. Enlil goes into the boat; Utnapishtim and his wife bow before
him. Enlil, now appeased, grants Utnapishtim immortality as a reward
for his loyalty to the gods.