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Now that I think on it, perhaps it's not the act of time travel in itself that creates the new timelines, it's the act of changing the past. We know in Ocarina of Time that the Song of Storms was part of a contained time loop, where Link had to go back in time and play the song so he could learn it, which frees up the sequence involving the bottom of the well (he's also responsible for unleashing Bongo Bongo, no less).

No, where Link really changes the timeline is probably when he steals the Silver Gauntlets. This wasn't a self-contained loop; if it were, we'd have to pick up the Gauntlets in the future, but also go back in time to obtain them so we could get them in the future. Instead he removes the Gauntlets from one timeline altogether. That is probably what created the third timeline, one where Link wasn't there to defeat Ganon.