The period saw large canals and changes to river systems, was it possible to continue building aqueducts and supplying cities with running water?
I'm afraid I can only speak in depth for a few cities in Early Modern England, but my main source does have a general overview, so I'll provide the general view first for most of Europe and go deeper on the English ones.
When discussing Early Modern aqueducts, we can consider two possible ancestries: They might either be a gravity-fed system from the Medieval era (and I have a post about them!), or a new-build system in the Early Modern, likely incorporating water-lifting devices of various types.
The great advantage of a gravity-fed Medieval-era aqueduct is quality. The builders of such aqueducts took great pains to secure water sources that could supply their locale and that were not polluted, and they also took similarly great pains to ensure that such water was not messed with on the distribution end. Refer to my previous post - note Siena's intricate arrangements for watering and laundry troughs, fines assessed, and especially my favourite bit, the riot in Viterbo over some people who thought it was a good idea to wash a puppy in the public fountain.
The problem is that as populations continued to expand, the old systems just couldn't keep up with demand. Assuming some of them were even working right - the South Gate Conduit in Exeter was perennially plagued with problems. It was built in 1554, but by 1559, was rather deficient, such that a complaint of that year notes that it hadn't had enough water to serve its intended recipients for three months, and over the years, was frequently the subject of complaint to Exeter's civic authorities. Gravity-feed systems were also difficult to build; you need a long run of pipe from the source to the distribution point, and that meant dealing with whoever owned the land the aqueduct had to run through, which needed money, influence, or political clout. With demand for water ever increasing, the Early Moderns needed something that could properly meet that demand.
Where the Medievals used springs and piped their water to the city, the Early Moderns turned to other systems. Water-lifting devices like waterwheels, pumps, or water-engines that combined both, meant that any water source was now fair game. You could simply install your water-engine, store the water in a water tower, and pipe that out for distribution. This dispensed with most of the need for lead piping, as wood pipes could fill most needs, and so gravity-fed systems had to compete with these water engines. (Aside: Our supplementary material for today is the noria. Loved them in Anno 1404, still love them in my studies. You really have to give it to the Muslims, they knew their water and hydraulic systems.)
Of course, since periodisation is always fuzzy, water-raising devices are not necessarily an Early Modern thing in themselves. Some north German towns already had water-lifting wheels by the late 1200s, and pumps started to become A Thing in Germany and Switzerland by the 1300s and 1400s. (Magnusson observes that water-engines were already in use to drain mineshafts by this time, and that there may well be a link between advances in mining technology and water-lifting devices for urban use.)
These devices crossed the Channel by the late 1400s, and in 1581, a waterwheel-and-pump engine was built on the first arch of London bridge, supplying water to residents of the eastern part of London by pipes. Exeter has record of a pump being used in its civic works around 1572, likely to drain out a part of either the underground vaults or one of the cisterns. By 1577, the city had installed a permanent pump at Rocks Lane to replace an old well there that was regarded as dangerous, and two years later, replaced the older conduit in front of the Guildhall in the middle of the city with a modern pump. Water-engines spread throughout the rest of England as well; Chester had one before 1635, while Exeter finished in 1698 a water-engine to supply the city.
One social difference in the English systems is that these water-engines were private devices, and thus anyone making use of them had to pay. Contrast those to the public conduits built by the Medievals, which were free to use; indeed, multiple testimonies about their purpose specifically note this: "for the public good of the citizens" (Exeter) and "for the general good and benefit of the town and inhabitants thereof" (Ipswich). You'd thus see a two-tier supply system in place in some English cities: wealthy inhabitants paid for private pipes from the water-engines, while those of less means relied on public conduits and other water sources. Indeed, Exeter maintained two spring-fed aqueducts throughout the 1700s specifically by popular demand. One observer even noted in the 1800s that water from the conduits "was considered the best for tea and pea-soup".
But remember the earlier note about the general better quality of the water from a Medieval-built system? The people definitely held that view, as we can see from the preferences expressed last paragraph. The water-engines almost always brought forth untreated river water, thus the consumers of such had a greater risk of contracting waterborne diseases. Indeed, most customers were aware that the water was of lesser quality, but considered the benefits to outweigh the costs. But since the Early Modern systems were easier to build and supplied more water, these came to displace many of the previous gravity-fed systems. A town that didn't have an aqueduct in the Medieval period very usually got one in the Early Modern, and those that did either replaced or supplemented them with Early Modern systems, as we've seen in Exeter. Those two spring-fed aqueducts we mentioned in Exeter? They were all that survived after 1700. Just ten years before, Exeter had six of them, only to discard four thanks to the new supply from the water-engine.
One should note that the conduits also fell for practical reasons. English conduits tend to be built in crossroads or in the middle of the street, the better to serve their locale. With vehicle traffic increasing as the years passed, the conduits came to be regarded as traffic obstructions, which helped in the decision to remove them later, in favour of new systems.
The cholera epidemics that struck England in 1848-1849 and 1853-1854 generated much consternation in Parliament, with several reports addressing water sanitation and purity, and these also called for municipally-sponsored conduits that were supplied by pure, external water sources. A Board of Health report issued in 1850 condemned the water quality supplied by private companies, and called for a supply of pure water under public management. (It is at this point that I giggle madly.)
That is, yes, the governments of the Early Modern period most assuredly had the technology and capability and financial capacity to build water supplies for their cities, as we can see from the English examples, and I don't doubt the rest of the Continent was able to do the same - indeed, given the lateness of water-engine adoption in England, I'm willing to say the Continent had more of them than England did at any given time. (And let us not discount the Dutch. They do strange things with water in the Low Countries. Polders. They made polders. Doubt not the Dutch when it comes to water.)
Water sauces:
Water Technology in the Middle Ages: Cities, Monasteries, and Waterworks after the Roman Empire, Roberta J Magnusson. This is just about my favourite history work ever, and I highly recommend it to anyone's and everyone's attention if you can at all get your hands on a copy. Whilst it's largely Medieval, Magnusson does include an epilogue about Early Modern systems, from which most of this post derives.
Water in the City: The Aqueducts & Underground Passages of Exeter, Mark Stoyle. If it's about Exeter or perhaps one of the nearby towns, it's from this book.