Okay, here we go:
The only museum in the Netherlands I can find about water treatment is the Watermuseum in Arnhem. Never visited it, mainly it’s more for educating children, nevertheless think it’s worth contacting them for your questions: [email protected]
About traditional hydraulic engineering there is in our country a lot to see for instance in the province of Zeeland as André already noticed. The Eastern Scheldt Storm Surge Barrier has a visitor centre where you can see why and how it is constructed, there are guided tours too. You need a car to get there. https://www.neeltjejans.nl/en/
Closer to Rotterdam the Maeslant Barrier is certainly worth a visit, there are guided tours in English (but at specific times). Interesting detail is that the concrete foundation of the barriers bal joint can move several centimeters giving enough flexibility to avoid overstress of the steel structure the time it’s closed during storm. You can get there with a car or public transport to Hoek van Holland and from there a taxi or rental bike. https://www.keringhuis.nl/english
The worlds larged inflatable dam is the Ramspol Barrier near the city of Kampen in the eastern part of the Netherlands. https://www.rijkswaterstaat.nl/english/index.aspx More north the Unesco listed “Woudagemaal” steam pumping station which still backs up if necessary. https://www.woudagemaal.nl/en
During war times the strategy of inundation was an effective way to keep the enemy away. The Nieuwe Hollandse Waterlinie east of Amsterdam is our nations most well-known defensive work based on this strategy. https://nieuwehollandsewaterlinie.nl/en/new-dutch-waterline/
The largest sea lock is now under construction in IJmuiden, SHIP is the visitor centre there, halas their website is in Dutch only. For guided tours contact: [email protected]
For a whole lot more about hydraulic engineering the Delft Univerity of Technology is the place to go. https://www.tudelft.nl/en/ceg/research/stories-of-science/
And last but not least Rijkswaterstaat, our Ministery of Infrastructure and Water Management takes care of most of the hydraulic works. https://www.rijkswaterstaat.nl/english/index.aspx