Make the crust: Preheat the oven to 325°F (163°C). In a medium bowl, combine graham cracker crumbs, sugar, and melted butter. Press the mixture into the bottom of a greased 9-inch springform pan. Set aside.
Prepare the rhubarb layer: In a small saucepan, combine chopped rhubarb, sugar, and water. Cook over medium heat until rhubarb is soft and mixture is slightly thickened. Let cool.
Prepare the cheesecake filling: In a large mixing bowl, beat the cream cheese and sugar until smooth. Add eggs and vanilla extract, mixing until combined.
Assemble the cheesecake: Pour the cheesecake filling over the crust. Spoon the rhubarb mixture on top and gently swirl it with a knife.
Bake: Bake for 45–50 minutes, or until the center is set. Let cool, then refrigerate for at least 4 hours or overnight.