In the first Spanish colonies how did nearly all American Indians die

The arrival of the Spaniards to the American continent produced a demographic disaster that caused the native population to decrease from approximately 20 million people before the arrival of the Spaniards in 1492 to only 4 million in the seventeenth century.

This was mainly due to the impact that the European arrival had on the spread of diseases such as smallpox, typhus, measles or influenza, to name just a few, for which the natives did not have any type of antibody (due to the isolation that they had respect to those virus strains produced in the European continent). This, coupled with the lack of development of medicine at the time and the lack of hygiene of some villages led to a pandemic spread and the annihilation of a large majority of the native population.

Answer: Almost all of the died because of wars or diseases brought over from the Spanish colonies.