Final answer:
The decline of the mission system in the 1600s was caused by diseases affecting Indigenous populations, exploitation of resources for the Spanish economy leading to environmental depletion and resistance-induced violence, and the destabilization of Indigenous cultures through imposed gender roles.
Step-by-step explanation:
The main reasons for the decline of the mission system in the 1600s include a variety of social, economic, and political factors. Illnesses and diseases brought by European contact devastated Indigenous populations, severely reducing the number of potential converts and laborers for the missions. Furthermore, the Spanish colonial economy aimed to funnel wealth back to Spain by exploiting local environments and resources, which caused environmental depletion and strained relationships with Indigenous peoples who depended on these resources. This exploitation often led to violence when Indigenous populations resisted the imposed economic conditions. On top of these issues, the restructuring of traditional gender roles among Indigenous peoples within the missions disrupted the economic and cultural stability of these Indigenous communities, which further contributed to the decline of the mission system.