Does the pipe go under the patio close to the house? It probably connects to your main house drain. The way these old drains work – very similar to a toilet – there is always standing water in the backyard drain, to prevent noxious gas from traveling out and stinking up the place. I found a diagram in an old plumbing manual once – will post it if I can find it again. The pipe may be clay, and broken. Best thing you can do is reroute your gutter into a rain garden. if that’s not possible, into a rain barrel or the alley. But if you see standing water in the drain, that’s normal.