In 1571 the Inquisition was fully established, the period marked, by the way, with a formidable eruption of Popocatepetl, and the next year the Jesuits arrived.

The matter of the Inquisition had been under discussion for many years, a council, as early as the year 1529, having solemnly declared it to be "most necessary that the Holy Office of the Inquisition shall be extended to this land, because of the commerce with strangers here carried on, and because of the many corsairs abounding upon our coasts, which strangers may bring their evil customs among both natives and Castilians, who, by the grace of God, should be kept free from heresy."

The full fruit of the declaration ripened only in 1570, when Don Pedro Moya de Contreras was appointed Inquisitor-General, with head-quarters in the city of Mexico. The Indians were especially exempted from its jurisdiction, only heretics from other nations falling under the ban.

The Quemadero, a burning place in the city of Mexico, upon land since included in the Alameda, was a square platform in a large open space, where the spectacle could be witnessed by the population. The first auto-da-fé was celebrated in the year 1574, when, as its chronicler mentions cheerfully, "there perished twenty-one pestilent Lutherans."

From this time such ceremonies were of frequent occurrence, but the Inquisition never reached the point it did in Old Spain. Although large numbers undoubtedly perished in these, autos-da-fé, the number of those actually burned to death was comparatively small and insignificant compared to that of the victims to this religious fury in Europe. Early in the present century the Holy Office was suppressed throughout Spain and all Spanish dependencies, and, although the Inquisition was again established, it was only for a short time.

Philip II. died just before the end of the century. With him ends the greatness of Spain, which from that time declined rapidly. Naturally the remote provinces felt the loosening of the firm hand which had controlled them, yet it is to be observed that the viceroys of New Spain under Philip III. were, for the most part, men of judgment and moderation. While the government at home, in the hands of profligate favorites, was growing weaker and weaker, that of Mexico was becoming more firmly established. Spanish blood had descended into a new generation, with Mexican habits, thoughts, and impressions. The national character, as always happens with colonists remote from their origin, was becoming modified into a new shape by change of climate and environment. Meanwhile the Indians were undoubtedly greatly improved by the genial influence of their new religion. They were like children, for it was not the intention of the Church to teach them to think, as they were only too ready to acquire the knowledge of how to obey.

In the beginning of the sixteenth century the city of Mexico was overwhelmed by inundations such as had from time to time caused the Aztecs great trouble. Their works were quite ineffectual against the floods which invaded the city, and it was evident that some vigorous measure must be taken. There was question, once more, of removing the whole city to the solid ground of Tacubaya; but this plan was open to great objections.

The engineer Enrico Martinez offered a plan for the rescue of the city which was accepted. It was to reduce the highest of the several lakes belonging to the network in the valley of Mexico, by diverting its waters elsewhere, and thus prevent its overflow. Work was begun in 1607. Fifteen thousand Indians were set to sinking shafts at intervals in order to bore a tunnel, to lead off the water, more than four miles long, and eleven feet wide by thirteen in height. It was completed in eleven months, and the event was celebrated by the presence of the viceroy himself with great pomp, who gave the first stroke with his spade. Mass was said, and there were great rejoicings. This cut was call the desaguë of Huehuetoca, a small village near the hills of Nochistongo.

The canal proved too small, and several schemes were tried for enlarging and strengthening it, with varying and moderate success. The novelty of the enterprise having worn out, people began to think, during a series of dry years, that the peril from the lakes after all was not so great. The engineer Adrian Boot was sent from Spain to visit the canal of Huehuetoca; having done so, he qualified it as insufficient, in which he shared the opinion of those who had not come so far. He failed in making it more efficacious, for, in 1629, came another inundation. In 1614, the rainy season having set in with unusual violence, Martinez, the engineer, himself gave orders to close the mouth of the tunnel, perhaps to rouse the people to its importance, and the importance of not neglecting it. The result was frightful. The whole city was instantly under water, and for five years it was converted into an unwilling Venice, during which the streets were passable only in boats.