It isn’t specifically about flooding. Flooding is a fairly manageable risk in the western Netherlands. As strange as it may sound for an area that is below sea level. The true problem for Gouda is its subsoil. The city is built on a thick peat layer, which is subsiding. Gouda is by far the most vulnerable historic city in that regard.
As you can see on the photo in the article, the water level in some canals is like 10 or 20 cm below the street level. Water so shallow will start creeping upward in your walls. The streets and to a lesser extent buildings are slowly subsiding. So why not just lower the water level? Well, this accelerates the oxidation and compression of peat, causing faster subsiding. You could heighten the street, but the extra weight will cause more subsidence. This is the conundrum Gouda is in.