The Ghost Ship only appears at night, so manipulating the Day/Night cycle is crucial in a speedrun in order to skip having to obtain the Song of Passing or needing to wait for the Ghost Ship to appear. The Ghost Ship also appears at different islands depending on the moon phase, and manipulating its location is also important. The time is measured in-game in terms of hours and minutes. 0:00 is defined as midnight, 6:00 is when it turns day, and 18:00 is when it turns night. The in-game date also advances by 1 whenever the time passes midnight.
Internally, the game keeps track of the time with a float between 0 and 360, but for ease of reading, we will be doing the conversion into the 24-hour system.
Time will never pass before you obtain the Wind Waker. After obtaining the Wind Waker, time passes differently depending on the current time. Between the times of 6:00 until 11:00 and 18:00 until 23:00, time passes everywhere normally on every island, including inside dungeons, buildings, and hidden caves. However, at any other times, time will not pass on certain islands. These islands include Windfall, Dragon Roost, Forest Haven, Outset, Gale, Headstone, Forsaken Fortress and Greatfish. Time will also not pass inside any building, dungeon, or hidden cave. Because of this, it is crucial to wait until it just turns day or night if you want time to pass at certain places, or arrive at a certain place before it turns day or night in order to have time freeze.
The time passes at a rate of 1 in-game minute every 12.5 frames, or 1 in-game hour every 25 seconds, or 1 in-game day every 10 minutes. Time does not pass at all until the wind waker is obtained. Events that reset the time to a specific value (see below) do still work though.
Occasionally, certain in-game events will reset the current time to a certain value. They are the following
Playing the Song of Passing will make it 12:00 if it were night, and 0:00 if it were day. The Song of Passing will always add a day if necessary.
Interestingly, time of day actually moves on the file selection screen, and it carries over into the intro cutscene. This doesn't matter since it gets reset when the transition to Outset occurs afterwards.
There is also a trick that allows you to go back to the previous day using the Greatfish cutscene. To perform it, superswim with double storage to Greatfish and pull out the wind waker to cancel camera lock exactly when the cutscene starts. This skips KoRL talking and the fadeout to endless night. The wind waker pull is frame perfect, making this TAS-only.
The Ghost Ship changes location depending on the day number/moon cycle. This is also the case with the Legendary Pictographs, which one is sold by Lenzo depends on this cycle also. Below are shown the correspondances.
| Week Days Cycle | |||
| Day | Moon Cycle | Ghost Ship Location | Legendary Pictographs |
| 0 | Waning Gibbous | Greatfish Isle | King of Hyrule |
| 1 | Full Moon | Crescent Moon Island | Ganondorf |
| 2 | Waxing Gibbous | Diamond Steppe | Great Fairy |
| 3 | First Quarter | Bomb Island | Jabun |
| 4 | Waxing Crescent | Spectacle Island | Queen of Fairies |
| 5 | Waning Crescent | Five Star Isles | Fado |
| 6 | Third Quarter | Star Belt Archipelago | Laruto |

Each Legendary Pictographs will only be sold if the corresponding character has been met by the player before.
The mail system also sometimes use the time system. In order to receive mail at all, Din's Pearl is required. Then to trigger mail, you generally need to meet a condition and sometimes also wait for the day to change. This is however not the case with all letters. Below are the requirements to obtain all the letters:
There are other interactions that check if the day has changed. For the most part, it is NPC dialogue that reset (Pompie & Vera for example). The Masked Beedle on Rock Spire checks how many days has passed since the first time you've talked to him, and he will do a "Grand Reopening" after 7 days. This is however purely flavor text.
There are however still some interactions that are useful to know: