Why did Hyrule flood? Was it the Gods? Or was it something more? I am writing this to explain a theory of why the "Gods" decided to flood Hyrule.
In Ocarina of Time. After Link defeated Ganondorf, he was given the choice to either stay as an adult or go back and enjoy his childhood. If he decided to go back to his childhood, this would eventually have him running into Termina. Because Termina is a parallel universe or rather, a different universe. The "Gods" had created an exact replica of Link just in case Ganondorf was to return. Like they didn't know where Link was? This brings up the question: Are there different Gods in Termina? One could assume that after Link left Hyrule that he was brought out of the Gods reach. If so, that may explain why the Triforce was unspoken or depicted in any way.
The Terminian Gods may actually be the Four Giants. Although they seem to be in an eternal slumber waiting to be asked forth in using there Godly might, the Giants are considered guardians, not deities, although they have been told to have created the world. But if one considers the term Deity, it may bring to mind the form of which Link takes from wearing the Fierce Deity Mask. The physical attributes Link acquires in this state could only be put as that of a Gods. Huge stature, tribal markings, an enchanted sword and his near invincibility.
The reason why you would think that he is too powerful is that his powers are in Link's grasp only during the Majora's Mask boss fight. The only way to counter this is by using a glitch that allows you to use it outside of the battle. When these requirements have been met, you can easily compare the drastic changes in the green heroes size to that of a normal Terminian. On the opposite side of the spectrum, you have Majora. Was the beast of which the mask was carved have been considered a Demonic being? All the factors explaining his personality point towards this. The Mask was sealed for eternity after being carved because of its extraordinary powers. At the end of the game, the happy mask salesmen gets his mask back, with it's power apparently drained and vanishes out of site forever.
When we take a look at Wind Waker, it's based several hundred years after the events of OoT. The prologue explains that the hero had saved Hyrule from darkness (Ganondorf and his reign) and leaves Hyrule in peace. However, it then begins to detail an evil coming back to Hyrule, unfortunately the hero didn't appear this time. Maybe this hero was too busy somewhere else, presumably Termina. This could support the theory of Link returning back to his childhood and soon visiting Termina. Leaving Hyrule off guard to dark forces, but what exactly are these dark forces? One theory could allude that the Happy Mask Salesman went back to Hyrule and used Majora's Mask to take over the kingdom. From this brings an even more realistic idea. In the events of TLoZ:MM Link has to stop the moon from crashing into Clock Town, destroying it. So if this were to happen again in Hyrule, what would be the consequences? Could the Moon have smashed into Lake Hylia or a bigger body of water to create a flood? or was it someone else, someone who wanted to gain revenge for meeting his terrible fate, someone who drowned?