Okay, Shmoopsters, we're just going to come right out and say this. Any time you see a reference to gardens (especially gardens that have been trashed) in Western literature, the author probably wants you to think about the biblical Garden of Eden, which, according to the Book of Genesis, was paradise on earth until it was ruined by Adam and Eve's fall from grace.
If you've read this play, then you know that gardens (literal and metaphorical) are all over the place in Richard II. The most obvious example is when the queen is strolling through her garden and finds out (from her gossipy gardener, of course) that her husband has lost the crown. Her response? She compares Richard's downfall to the Biblical fall of man:
Thou, old Adam's likeness, set to dress this garden,
How dares thy harsh rude tongue sound this unpleasing news?
What Eve, what serpent, hath suggested thee
To make a second fall of cursed man?
Why dost thou say King Richard is deposed?
Darest thou, thou little better thing than earth,
Divine his downfall? Say, where, when, and how,
Camest thou by this ill tidings? speak, thou wretch. (3.4.8)
The queen is pretty irrational here. She's acting like the Gardener has caused the "second fall" of man just by gossiping about King Richard being deposed (bumped off the throne). Even though the queen's logic is a little wacky, we can tell that Shakespeare is making a bigger point: the idea is that deposing a king is a sin (especially for those who think kings are appointed by God). That means there are going to be some serious consequences that will change the world (read: England) forever – just like Adam and Eve's world was changed forever when they blew it by giving in to temptation. We find out what these consequences are in the sequels to this play: Henry IV Part 1, Henry IV Part 2, and Henry V.
But whose fault is it that England is (or will be soon) like a ruined garden of Eden? Most characters in this play blame Richard. Don't just take our word for it – let's think about what the Gardener has to say. Earlier, in Act 3, Scene 4, the Gardener explicitly compares the kingdom with a garden and suggests that Richard hasn't been a very good gardener. He hasn't pruned it, he hasn't weeded it, he hasn't bothered to take care of it. He's assumed, instead, that it would take care of itself, or that God would take care of it. The problem with this logic is that it doesn't take into account the fact that gardening (like kingship) is not a passive activity: you have to till; you have to earn your crop.
Not only that, but Richard has surrounded himself with lousy advisors, like Bushy, Bagot, and Green, who would rather flatter him than give him honest feedback about how to run the country. This is why Henry Bolingbroke refers to Bushy, Bagot, and Green as "caterpillars of the commonwealth" (2.3.11). The metaphor implies that Richard's advisors are a bunch of parasites devouring or destroying England, just like pests might destroy a garden.
Add to this the fact that Richard has "farmed out" or "leased" the land in order to raise money. Gaunt tells him that his decision made him a "landowner" instead of a king. Future events seem to bear this out: by basically mortgaging the land, Richard mortgages his kingdom. John of Gaunt reminds us of this when he cries that Richard mismanaged "this other Eden, demi-paradise," this "blessed plot, this earth" (2.1.3).
Of course, after Richard's death, some characters see things differently. In Henry IV Part 1, a guy named Hotspur refers to Richard II as a "sweet lovely rose" who was uprooted and replaced by "this thorn, this canker, Bolingbroke" (Henry IV Part 1, 1.3.7). In other words, Hotspur also thinks of England as a garden, but he believes it has been ruined by Bolingbroke (a.k.a. Henry IV), not Richard.
Brain Snack: Can't get enough of Shakespeare's obsession with gardens? Go talk to Hamlet, who sees the whole world as a smelly, "unweeded garden that grows to seed" (Hamlet, 1.2.6).