I heard a little about it in school, but otherwise has no clue. They were treated similarly to the Jews, apparently.
The Nazis didn't want to exterminate Jehovah's Witnesses. JW were persecuted and imprisoned in Concentration Camps but not targeted for systematic murder.
The Nazis also didn't target all JWs, but rather people they called "Ernste Bibelforscher", which included JWs, Seven Day Adventists, and the so-called Free Bible-Students, which were an offshoot of the JWs and Adventists. The main reasons these groups were persecuted was that they rejected that state and especially military service and that they continued to try to convert people to their religion that had been outlawed (because of the military service thing) in 1935. In the Nazi logic, refusing to join the military and to swear oaths on the Führer amounted basically to treason against your race and thus these groups, the Bible-Students, were considered a small but nonetheless serious problem.
Those imprisoned in Concentration Camps were mostly those who continued missionary duty and who actively rejected military service. Little research has been done into this but it seems that there was a small number of JWs and Seven Day Adventists drafted into the Wehrmacht serving without weapons, so those who were persecuted were those who actively and publicly rejected serving.
In the Concentration Camps, we see two distinct phases on how the JWs were dealt with. Up until 1941, the regime for them was especially harsh. The idea behind it given out by the Inspector of the Concentration Camps was to make them repent through violence and harsh treatment. JWs and other Bible-Student prisoners could be released from the camps if they renounced their faith and joined the Wehrmacht. The camp administration often tried to achieve this by treating them especially brutal and forcing them to do work against their religion (i.e. working in an ammunition's factory) and killing or beating them if they refused.
Their treatment changed around 1941 however. With the camp system becoming larger and larger and also involving itself more and more in economic activity, prisoners were needed for work details that took place outside of the camp area and where the Nazis -- rightly -- suspected that the danger of prisoners escaping was rather high. That is for all prisoners except the Bible-Students. Even if given the chance, the Bible-Student prisoners would not escape the camps. In their faith, imprisonment in the camps was basically a test from God for the coming end times and while they refused any cooperation with the war effort, they also refused to flee. Theological debates took place in the cams surrounding this in illegally printed watchtower leaflets. Anyways, once the camp administration figured this out, they used the Bible-Students as preferred prisoners for work details outside the camps. In Austria, one such detail e.g. fixed up a farm house for a high ranking Nazi where the prisoners also slept in said farm house with only one guard. They could have overwhelmed him but stayed put.
Similarly, the Bible-Student prisoners were also favorites among the other prisoners because if they were in charge of a work detail, they would not beat their fellow prisoners even if ordered to.
So, to sum up: JWs and other similar groups were targeted because their pacifism and refusal to cooperate with the state was seen as dangerous. They were not targeted for extermination but rather imprisoned if active in their faith and treated brutally in at first in order to get them to renounce. Later on, the Camp administration improved their situation because they figured out that as far as theologically permitted, the Bible-Student made for cooperative prisoners.
We don't know exactly how many Bible-Students were imprisoned or killed in the Camps but in Auschwitz the number of Bible Student prisoner was 387 and it was the biggest JW prisoner population in the Camp System.
Detlef Garbe: Zwischen Widerstand und Martyrium. Die Zeugen Jehovas im „Dritten Reich“. In: Studien zur Zeitgeschichte. 4. Auflage. Band 42. Oldenbourg, München 1999.
Michael H. Kater: Die Ernsten Bibelforscher im Dritten Reich. In: Vierteljahrshefte für Zeitgeschichte. Nr. 2, 1969.
M. James Penton: Jehovah's Witnesses and the Third Reich. Sectarian politics under persecution. University of Toronto Press, Toronto 2004.