It had a terrible effect on the Natives. The Spanish and Natives did not get along well at all, and since the Natives were not very advanced in weaponry, etc, many of them endured constant suffering and became slaves. A lot of Natives died during battles as like I said, the Spanish were very much more advanced than them. Also, since the Natives were protected from diseases, the Spanish brought over tons of illnesses which also killed a lot of the Native Americans.