Both the Water Tribes and the Earth Kingdom suffered in a critical manner, making it impossible to determine which was affected more.
Due to the war, the Southern Water Tribe was nearly wiped out, along with its traditions and culture. The removal of waterbenders from the tribe proved to have a heavy effect on it, making it nearly impossible to rebuild. Although the Northern Water Tribe kept untouched for the most part, they lost their tribal princess and the original moon spirit.
In the case of the Earth Kingdom, the majority of it was conquered and enslaved by the Fire Nation. A large amount of citizens were killed in battle, or by other means. Civilizations were destroyed, or ravaged to a point of poverty. The previously unconquered Ba Sing Se fell for the first time, as well.