Pigmentation dispersal

Pigmentation dispersal could cause the eye to change colour.

When a Rutan mothership exploded over Fang Rock, Leela turned, against the Fourth Doctor's instructions, and saw the blast. The flash prompted pigmentation dispersal which changed the colour of her eyes from brown to blue and left her temporarily blind. (TV: Horror of Fang Rock)

Leela was again blinded by the premature detonation of a percussion grenade in the Artron Forum and believed that she would again recover and have a different eye colour. President Romana, however, told her that her eyes had not changed colour and Elbon told her bluntly that the damage was permanent. (AUDIO: Fractures)

Behind the scenes
Louise Jameson found the brown contact lenses she wore as Leela extremely uncomfortable and seriously considered leaving the show as a result. Therefore, for Season 15 the production team created an in-universe explanation that allowed her to play Leela with her natural eye colour.