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According to The river sea : the Amazon in history, myth, and legend, page 112,

In any study of these wild regions [of South America], one is constantly astounded, even moved, regardless of one's religion or lack of it, by the dedication and bravery of the Spanish friars who established missions in some of the most isolated and inhospitable spots on earth. There was an obverse side to their ministrations, however. They controlled the only viable routes into the interior of South America and for three centuries were able to block exploration.

One is not used to thinking of friars as being armed, let alone having enough military force to be able to sink any ship attempting to sail up a miles-wide river, which is what would seem to be required to block exploration up the Amazon and its major tributaries. So how exactly did they do such controlling and blocking?

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    Perhaps they would just refuse to provision anyone looking to go further upriver?
    – T.E.D.
    Commented Oct 5, 2020 at 2:59
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    Maybe they just had to say 'No'. They were priests and, as such, had a certain authority which most explorers were not prepared to challenge (either out of respect for the church or out of fear of possible repercussions when their disobedience was reported to higher authorities). Commented Oct 5, 2020 at 4:24
  • mmm ... such is the "business" of God.
    – Fred
    Commented Oct 5, 2020 at 9:37
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    are you sure the source refers to the Amazon? In the Portuguese side, it would be very hard to block the large rivers with no navy. This could make some sense regarding the jesuit missions among the Guarani and Tupi in Paraguay and South Brazil - the tribes were armed and had some official backing to keep outsiders away, but it did not last 3 centuries. But in the Amazon? Besides that, the Andes and the Portuguese, who got much of the amazon basin, were much more formidable obstacles. Yet, your source may know something about the Spanish part of the Amazon basin that I do not know much about.
    – Luiz
    Commented Oct 5, 2020 at 14:27

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