Naboo was a geologically unique world in the galaxy. A plasmic molten outer core surrounded an inner core, believed to be composed primarily of a nickel-iron alloy, with very small amounts of some other elements. These elements were found in abundance in other chemical compositions in the galaxy, but it is the unique properties of the plasma which interested astrophysicists, plasma which the two primary civilizations harnessed to supply clean and efficient energy highly valued throughout the galaxy.
The plasmic magma "seethes and bubbles" from the center of the planet carving labyrinths of winding tunnels and caverns similar to lava tubes of traditional magma flows. Much of these abyssal labyrinths were submerged in great underground oceans, which were home to immense aquatic animals and creatures that were never seen on the surface. Animals such as the colo claw fish, opee sea killer, sando aqua monster and others inhabited this underworld realm. Gungans dominated these "underwaterways," using them as a highway of sorts between their surface Holy Places and their underwater cities. The Gungans also used these tunnels for trading between Bubble cities.
Plasmic eruptions found their way to the porous crust of the planet, affecting geographic features there such as mountain chains and plate tectonics.
The surface of Naboo was covered by dense swamps, rolling grass plains, seas and verdant hills. The largest mountain chain, the Gallo Mountains, bisected the largest continent and divided the great grass plains of the north from the Lianorm Swamp and bayous in the south. South of the Lianorm Swamp was the great Paonga Sea, where at the bottom lay the Gungan city of Otoh Gunga. The Lake Country was an area known for its natural beauty, and was home to many vacation estates.
The Gungans were believed to be indigenous to Naboo, but this is uncertain. They have been there a long time, as they engaged in battles of survival with the veermoks during an ice age.
An alien civilization of reptilian humanoids remembered as the "Elders" colonized Naboo. Around 7,032 BBY, they engaged in warfare with the Gungans, forcing the Gungans to retreat underwater, giving rise to modern Gungan civilization. Monuments and ruins, scattered throughout the planet, were built by the Elders. The largest of these ruins, located on the northern edge of the Lianorm Swamp, was identified as the Gungan Holy Place. The Gungans viewed these ruins as sacred, and their builders as "guds". Both Gungan and Human Naboo scientists agreed that the end of the "Elder" civilization, 5,032 BBY, may have been the result of the "Elders" negligence towards their environment.
The Ankura and Otolla branches of Gungans united, forming a symbiotic relationship. They dominated Naboo for millennia afterwards, though largely keeping to the swamps and waterways; the mountains and grasslands considered 'desert-like' for them.
Around 3,951 BBY, prior to the end of the Sith Civil War, Elsinoré den Tasia ascended to the throne of the Core World of Grizmallt. She sponsored the Republic explorer Kwilaan, who discovered Naboo with a fleet of three ships—Beneficent Tasia, Constant and Mother Vima. The planet became known as Naboo, after the deity Nabu. Naboo quickly became notorious amongst big game hunters who favored the indigenous veermoks, although it would be five decades before permanent Human settlement.
Eventually, in approximately 3,900 BBY, Human refugees fleeing a violent revolution on Grizmallt, led by none other than Kwilaan, settled in the mountains and great grass plains. Cultural differences led to tension between the two peoples—but direct conflict was rare. Over time, there was more conflict between the various Human settlements than between the Human nation of Naboo and Gungans.
The Gungans long lived in rival cities. In 3,000 BBY, a warlord known as Rogoe destroyed Otoh Sancture using Bursas. Boss Gallo escaped this destruction, being on a hunt at the time to provide food for a feast. Gallo united the thieves under rogue Captain Marsune and the various Gungan cities' defense forces to form the Gungan Grand Army. Gallo and Marsune led the Army to conquer Rogoe's capital, Spearhead, which he renamed Otoh Gunga—a city for all the Gungans. The Bosses of Otoh Gunga, including Gallo's descendant Rugor Nass, maintained a hierarchical leadership over the Bosses of the other cities thenceforth.