The Goddess of Time was first mentioned in the flashback of Majora's Mask, when Link first meets the Skull Kid atop the Clock Tower. In the flashback Zelda shows Link how to play the Song of Time. She says "The Goddess of Time is protecting you. When you play the Song of Time, she will aid you...".
As one of the more mysterious of theories in the Zelda Universe, the identity of the Goddess of Time is difficult to pin down to one explanation. Many have theorized that it is none other than Nayru, the Goddess of Wisdom, while some contend that is could not possibly be one of the Golden Goddesses, as each of them already have a defining characteristic. While it is not unusual for a character to represent themes of two goddesses (such as Laruto, the Zora Earth Sage of Wind Waker, it is also possible that "Goddess of Time" is nothing more than a personified name given to time, as "Mother Nature" is often the name used for the forces of growth and vitality. Here we consider the evidences for the most likely candidates of the title "Goddess of Time."
Evidence for Nayru
Temple of Time, Oracle of Ages, Goddess of the Sand (Desert Colossus and Arbiter's Grounds)
Perhaps the strongest evidence for Nayru as the Goddess of Time is her connection to the Hylian race. The Temple of Time, a Hylian edifice, is almost certainly dedicated to the Goddess of Time and if any of the Golden Goddesses could be given the title for this reason it is Nayru. This evidence may not be sufficient, however, as the Temple of Time may be named not for the Goddess of Time, but the Hero of Time, who would one day draw the Master Sword from its pedestal and travel through time to save Hyrule.
The next most obvious connection is that Nayru is the namesake of the Oracle of Ages, whose Harp of Ages permits Link to travel through time. The oracle Nayru may also travel through time freely herself, thus reinforcing her association with this attribute. This argument is problematic, however, as the other two goddesses ought to bear the attributes of the oracles who bear their names. While Farore may be associated with secrets (like the Oracle of Secrets by the same name), in no other instances than this one has Din been attributed with the passing of the seasons (as is the power of the Rod of Seasons, an item associated with the oracle Din). The latter becomes even more troublesome when one considers that the passing of the seasons is also a passing of time, in fact showing that either Din or Nayru could be the Goddess of Time based on the Oracle/Goddess theory.
A third piece of evidence that is as helpful as it is cumbersome is the statue of the mysterious Goddess of the Sand in both the Desert Colossus and the Arbiter’s Grounds. This statue of an unnamed goddess is often depicted entwined with a huge serpent. This detail resembles Lanayru, the Light Spirit in Twilight Princess, whose form is that of a giant crocodile-headed snake. As Lanayru is the representative Light Spirit of Nayru, these connections may associate the buildings with the Goddess of Wisdom. Further, if one views sand as a metaphor for time (as in an hourglass) then the statue of this sand-goddess may represent the elusive Goddess of Time, and therefore Nayru.
Evidence for Farore
Ciela, Link as Hero of Time
Link, Hero of Time and Chosen of Courage
In Phantom hourglass, the fairy Ciela is revealed as the Spirit of Courage and Time. Further, in Ocarina of Time, Link becomes the Chosen of Courage and the Hero of Time. It may be that these two attributes are connected and, by extension, their source is the same. While not conclusive, this is enough evidence to suggest that Farore may be the Goddess of Time.
Evidence for Din
Oracle of Seasons, Goddess of the Sand (Desert Colossus and Arbiter’s Grounds)
Depending on how they are viewed, two of Nayru’s evidences could be used to show that Din, and not Nayru, is the Goddess of Time.
As stated above, the Oracles of Seasons and Ages share attributes that suggest power over time; the ability to change the seasons and travel through time, respectively. Because of this, either Din or Nayru could be attributed with the Goddess of Time by virtue of the Oracle/Goddess theory.
Likewise, if one considers Din’s connection with the Gerudo people as similar to Nayru’s connection to the Hylia, then one could draw a parallel between Nayru’s connection to the Temple of Time and Din’s connection to the Desert Colossus and the Arbiter’s Grounds. While not having any direct connection with snakes, Din is strongly associated with fire (as the spell Din’s Fire). In the Arbiter’s Grounds, the Goddess of the Sand is depicted holding fire in each hand, and in the Desert Colossus the goddess’ statue holds a chest in one hand surrounded by a circle of fire (until Link activates a switch in the other hand). All of these evidences point toward Din’s association with the Goddess of the Sand, and therefore any further connection with the Goddess of Time.
Evidence for a fourth goddess
Ordona, Temple of Time, missing Triforce?
Despite evidences to the contrary, the true identity of the Goddess of Time may in fact be another goddess not mentioned in the creation myth of Hyrule. It is clear from the statements of Princess Zelda and the fairy Tatl in Majora’s Mask that the Goddess of Time was known at least to these two characters, but no other characters mention the goddess by this title, and no connection with the three Golden Goddesses is explicit. For these reasons it is not unreasonable to investigate the possibility of a fourth, less-well-known goddess whose sole theme is time.
The foremost evidence for a fourth goddess is the presence of four Light Spirits in Twilight Princess. Three of these Light Spirits were instrumental in the sealing away of the Fused Shadow’s powers when three “Dark Interlopers” tried to steal the Triforce. Each of the three Golden Goddesses has a representative Spirit with a corresponding name; Lanayru for Nayru, Eldin for Din, and Faron for Farore. While some theorize that Ordona’s name represents the latter portion of “Farore”, this is not conclusive, and at any rate would create an imbalance in representation, giving the Goddess of Courage two Light Spirits instead of one. What is perhaps more likely is that there is a fourth goddess, with a name resembling Ordona’s in part, who was not involved with the sealing of the Fused Shadow’s power. It could be that this anomalous Light Spirit represents the Goddess of Time.
Ocarina of Time
Following this train of logic, one might consider the form of the Triforce itself to add insight to the Ordona/Goddess theory. The Triforce is made of three triangles which form a larger triangle. However, upon closer inspection this symbol reveals a fourth, inverted triangle; the negative space in the center of these three. Like the Light Spirits, where four exist but one is not always present, so the Triforce may have been originally composed of four pieces and this fourth triangle is like a missing piece. As each piece of the Triforce is aligned to one of the Golden Goddesses, then the existence of a fourth, missing piece could mean that the goddess whose piece was missing might not be known by the denizens of Hyrule at large. This angle on the theory would explain why few are privy to the Goddess of Time’s existence, and yet the artifacts and sacred places aligned with her (like the Ocarina of Time and Temple of Time) are still around to prove that she once had a place in Hyrule.
If we permit the idea of a fourth goddess, it may be assumed that any and all of the appropriately named collateral were inspired by her or created by her followers. The Temple of Time would have been where her adherents went to worship her. The Ocarina of Time would have been blessed by her. The Song of Time would have been sung in her honor. Even the Pedestal of Time, so called, would have been prepared to bear the Master Sword with the Goddess’ champion, the Hero of Time, in mind.
Conclusion
Along with the nature of the elusive Dark Tribe, the true identity of the Goddess of Time may very well be one of the more complex and baffling mysteries of the Zelda series. What is certain is that Zelda fans will continue to theorize until Nintendo reveals their well-kept secrets. Until then, it can be said that Nayru is the safest (if not most probable) candidate for the title "Goddess of Time."