Millbrook Marsh is located approximately in the geographic center of the Spring Creek Watershed (Map 2 - Spring Creek Watershed), within the ecoregion known as the Ridge and Valley section of the Appalachian Mountains. Bathgate Spring Run and Thompson Run flow through the marsh leading into Slab Cabin Run, which then joins Spring Creek a short distance from Millbrook. Spring Creek, which begins on Tussey Mountain and ends in Milesburg, is a tributary of Bald Eagle Creek. Spring Creek and 6 other major tributaries contribute to Bald Eagle Creek before it enters the West Branch of the Susquehanna River, the primary river supporting the Chesapeake Bay.
The climate of the region is considered to be a humid continental type. Precipitation is ample, with an average of about 1016 mm (40 in) annually. About half of that falls as rain during the 166 day growing season. Winter months usually bring 762 to 1524 mm (30 to 60 in) of snow. Temperatures are generally below 0° Celsius (32° Fahrenheit) from November through March, but very seldom reach below 17.7° C (0° F). From June through August, the temperature is usually in the upper 20’s Celsius (low 80’s Fahrenheit) during the day and near 15° C (60° F) at night, with about 15 hr of sunlight per day.