The water divide between Fulda and Werra draining into the Weser, and the Fränkische Saale, draining via the Main into the Rhine, runs over the Rhön mountains.

In the underground of the Rhön, mainly bedrock-aquifers (fractured aquifers) are found. Due to its tectonic, faults of plates and rift margins, and the character of its bedrock, the ground water displays a high productivity. In the high altitudes of the Rhön, tertiary fractured aquifers of a low permeability are found. These are of vulcanic origin (basalt layer), and predominatly resting on rock layers of the Middle Red Sandstone. They can be characterized as perched aquifers. Because of a usually rather thin overburden, the filtration of ground and spring water is not very thoroughly, the water quality has thus to be classified as threatened.

The ground and spring waters of the Rhön are used locally for drinking water supply. Especially the Bavarian and Hessian communes in the Biosphere reserve are exclusively pumping water from local ground water sources, mostely tapping springs. On a commercial scale, drinking water is pumped from wells by the regional based mineral water industry. These are promoting their connection with the biosphere reserve in commercials and marketing.