What problems did Spanish colonists in New Mexico face ?

The early settlement of New Mexico by the Spanish was characterized as a constant struggle with the Native American populations in the region.  Aside from the challenging hot climate that sometimes produced  drought and difficulty for farming, the major problem for the colonists was the conflict with Indians.  New Mexico grew slowly as a colony of Spain and was primarily a Spanish mission that attempted to convert the Pueblo Indians.  The Pueblo had very little interest in abandoning their religious ceremonies and rebelled against Spanish interference in 1680.  The Spanish would leave the area for a decade before returning to reclaim New Mexico.  They attempted a peaceful resolve but ended up attacking the Pueblo.  The Spanish and Pueblo would form an alliance, but there was no shortage of Native American tribes to threaten the Spanish colonies.  The Comanche and Apache were the most serious threat, but the Spanish were surrounded on all sides by hostile Indian tribes.  Conflict with these tribes would be a legacy of Spanish rule in New Mexico.