Combine cranberries and water in a large saucepan; bring to a boil. Reduce heat; cook 5 minutes or until the cranberries have popped.
Combine sugar, flour, cinnamon, nutmeg, and salt; add to cranberries. Cook over medium heat, stirring constantly, until thickened. Stir in butter and apples. Remove mixture from heat, and cool.
Roll half of pastry to 1/8-inch thickness on a lightly floured surface; fit into a 9-inch pie plate. Spoon cooled filling into pastry shell.
Roll remaining pastry to 1/8- inch thickness, and place over filling. Trim edges; seal and flute. Cut slits in top crust to allow steam to escape.
Bake at 375° for 55 minutes or until crust is lightly browned. Cool before serving.
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