How to extrapolate meaningless interpretations from tiny bits of canon: Applejack was under the surface of the mud pit with no breathing apparatus from 17:50 to 19:42, or approximately 1:52. Ponies are generally assumed to reach about waist-stomach height on an adult human of average height (judging based on fanon interpretation, as well as the respective heights of the children and ponies in previous generations), but have slightly larger chests in comparison to overall body size. For the purposes of this, we can assume that the average pony would have something on the order of 65-85% of the lung capacity of an adult human, but if we account for Earth Pony magically strengthened endurance, it should be roughly equal. Now, the average human is able to hold their breath for 30s-60s while submerged. However, it is possible to train yourself to hold your breath for longer periods of time, particularly if you are in a line of work which requires you to spend substantial lengths of time in and under water. The current record for longest breath held underwater by a human is 18m32.59s by Brazilian Karoline Mariechen Meyer. In other words, Applejack held her breath more than twice as long as the average for a normal pony, despite having no need to do so once the switch had been made. She also somehow managed to detect that the race was over, despite being submerged in mud that was thick enough to provide a sufficiently solid surface for Sweetie Belle to jump across. After emerging from the mud, she displayed no sign of panic or serious O2 deprivation, needing little more than a quick, deep breath before hopping out and trotting over to her friends.
Therefore, the only rational conclusion is that Applejack is a former member of Equestria's elite aquatic Special Operations organization, Bay Watch, which has long been at the forefront of the secret war against the terrible threat of the godless pinko Seaponies and their musical weapons of mass destruction.
lolhorsepun