The Reformation movement of the 16th and 17th centuries were incredibly disruptive to Europe. Consider that Europe had been mostly under the thumb of the Catholic Church for a millennium. Once new denominations began to take hold around the continent, infighting, revolts, and repression resulted.
Civil wars were common as Catholics and Protestants vied for power. France alone experienced over one million deaths as a result of these conflicts in the latter part of the 16th century. The French reform wars largely ended in 1598 when King Henry IV issued the Edict of Nantes, which granted religious freedom in his kingdom. However, in 1685, King Louis XIV revoked the edict which led to the persecution and slaughter of thousands of Huguenots. Most of the survivors fled the country.
These religious upheavals also led to the spread of nationalism around the continent. As kingdoms and local principalities adopted different sects and denominations, more of a national identity arose. This led to state religions which were closely tied to national identity. The influence of monarchs grew, as they often became the head of their state's official church. Even the rulers of many Catholic kingdoms followed suit and moved further away from the influence of the Vatican. Because of this, this period is sometimes referred to as "The Age of Kings and Queens."
Migrations were also a result of these upheavals. As it became increasingly more dangerous for adherents of a particular denomination to remain in a country in which they faced persecution, they often left for places in which they could practice and live freely. Protestants in France went to Switzerland and the Netherlands. Germans moved from one principality to another. It even fostered trans-Atlantic migrations, as Puritans from England set sail for the New World in search of a land free from the excesses and authority of the Anglican Church.
As you can see, the very nature of Europe was forever changed by the Reformation and the religious upheavals that were a part of it.