In Satya Yuga, Manu creates a boat to save the 7 sages from the great deluge/flood and Lord Vishnu assumes the avatar called as Matsya avatar and pulls the boat.
But why does the great deluge/flood happen?
First have a look at this excerpt:
"When Brahma goes to sleep in the (Brahma's) night, all planetary systems below his abode, Brahmaloka, are inundated with water. He dreams about Maha Vishnu who gives him instructions to rejuvenate the universe again."
Then look at the concise summary of the story of the seven sages, sailing through the flood:
Matsya-Vishnu declared that a great flood would come seven days from then and engulf the universe. He ordered Satyavrata to assemble the seven great sages and with their counsel, gather all kinds of seeds, herbs and various beings to load them on a boat, that would be sent by Vishnu on the fateful day. He instructed that the serpent Vasuki should be used as a rope to tie the boat to his fish-horn. Promising that he would sail the boat through the waters throughout the night of Brahma, Matsya disappeared after his revelation and reappeared as a horned fish on the day of the Deluge, when torrential rains drenched the earth.
So it is possible the whole legend relating the deluge/flood should be taken symbolically. And the answer as to why the flood happens, is because Brahma goes to sleep? Note: One night of Brahma is commonly seen as consisting of 1 kalpa (8.64 billion human years), a period that happens after the day of brahma, also consisting as one kalpa (source).