Yes they will as your graduating GPA will be an accumulative average of all 4 years of high school, but colleges also look at each year too, so it will be what it is.
If I had a 2.5 gpa freshman year, a 2.8 gpa sophomore year and then raised it to a 3.9 junior year and am taking all AP classes senior year, will those other two bad years of highschool count towards college?