The site of Hylia Marine was first settled by High Zorans traveling down the Zora River from the Dominion Valley. Considering Lake Hylia to be sacred, they constructed the Water Temple underneath a large island off the northern lake shore. Traditionally, even into the modern era, a small detachment of Domain troops remain to guard the Temple. Due to its distance from the Dominion, however, the Lake was never properly settled by Zora, and in the time of Akkala numerous villages and holds dotted its northern shoreline. The area of Hylia Marine became a gathering place for Akkalans and Zora to meet, and over time the Zora Dominion abandoned any claim to the area and a Hylian port town grew up around the bridge and Water Temple.
In 1 BG, during the Rise of Ganon, King Sil Rhoam Bosphoramus had the Triforce hidden within the Water Temple to protect it from Ganon's invading Moblin armies. Using the Eye of Truth, the Druthulidi Dethl, possessing the Yiga Mage Bongo, learned the Triforce's location and misdirected Ganon to hunt for it at Death Mountain while she and her Yiga forces set out to take it for themselves, defeating the token Zora garrison at Hylia Marine and occupying the town. By 1 AG, to Dethl's surprise, the criminal Great Fairy Veran and the Twinrova sisters, Koume and Kotake, also realized where the Triforce was located, and set out with their own renegade armies to claim it, leading to a three-way conflict that devastated the town. Meanwhile, the Dominion dispatched a relief force to support their temple garrison, led by General Rutela. With the aid of the Hylian Princess Nylin Nohansen Zelda I and her tenuous new ally, the Druthulidi Demise, the Zora managed to route all three armies and capture their leaders, ending the war.
The city was rebuilt during Nylin's reign, returning to its role as Lake Hylia's only port, as well as a pilgrimage site and popular fishing and retreat destination.