Bring a large pot of water to a boil over high heat. Stir in the shell pasta, and return to a boil. Cook the pasta uncovered, until just slightly firm to the bite, about 13 minutes. Drain well.
Brown the ground beef in a large skillet; drain fat. Stir in the taco seasoning and water; cook over low heat until thickened, about 5 minutes. Stir the refried beans and 3/4 cup Cheddar cheese into the taco meat. Spoon meat mixture into prepared pasta shells.
Spoon 1/4 cup salsa over the bottom of a 9x13 inch baking dish. Arrange filled shells over salsa. Spoon remaining salsa over shells.
Bake in preheated oven for 40 minutes. Remove from oven; sprinkle with sliced green onion and 1/4 cup shredded Cheddar cheese. Serve with sour cream.