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?