The phrase "almost natural" spoken by Maria to Sir Toby in Act 1, Scene 3, in relation to Sir Andrew, is a pun on the word "nature" that Sir Toby uses in the line just above this. In this scene, Maria is scolding Sir Toby and warning him that Olivia dislikes his drinking habits. She also scolds him for bringing to the house his drinking buddy, Sir Andrew, as a suitor for Olivia. In the lines prior to the line in question, Maria calls Sir Andrew foolish and wasteful with money, while Sir Toby tries to defend Sir Andrew's character, saying that he can play an instrument, is fluent in four different languages, and "hath all the good gifts of nature," which means that he is blessed by nature, possibly specifically referring to his being handsome (25).
Maria, in reply, makes a pun using the word nature in her line, "He hath indeed, almost natural" (26). In Elizabethan times, the word natural was also used as a slang term to mean idiot (eNotes). Hence, the word nature is being used with two different meanings, making the word "natural" a pun. The first meaning is Sir Toby's meaning, what comes naturally, such as innate qualities like good looks, while Maria uses it to mean idiot. Maria then proceeds to list all of the ways in which Sir Andrew is an idiot, such as being both argumentative and a coward.