Batavia Kill begins on the north-northeast slopes of Blackhead Mountain and starts travelling northwest as it gains an unnamed tributary draining northeast slopes of Black Dome. The kill continues northwest and gains an unnamed tributary draining the southwest slopes of Acra Point. It slowly curves southwest as it descends the Black Dome Valley and enters the hamlet of Maplecrest, where it curves back to the northwest. The creek then passes through Hensonville, passes under New York State Route 296 as it curves to the west, and begins to parallel New York State Route 23. It then enters the hamlet of Windham, where it receives Mitchell Hollow Brook from the north. It continues paralleling New York State Route 23 as it enters the town of Ashland. It soon enters the hamlet of Ashland, where it receives Sutton Hollow Brook from the north. The kill continues westward and soon receives Lewis Creek from the north. The kill then enters the town of Prattsville and soon flows over Red Falls by the hamlet of the same name. Batavia Kill then curves to the southwest, crosses under New York State Route 23A, then converges with Schoharie Creek southeast of the hamlet of Prattsville.