My employer has just informed me that the business will be relocating to a different city in the Netherlands. I'm also planning to move house soon, which will mean that the commute to the office will be significantly longer. Unfortunately, I have to be in the office on a daily basis so can't even work from home. I have discussed my concern with my manager and she has now asked me to think this through carefully and whether this will be ok for me going forward or if it will cause issues for myself and the company. I have a feeling that she implies that I can either accept the change or resign - can my employer do this?
There's no default assumption in Dutch Law stating that this is either allowed or disallowed; each case has to be considered individually.
In your case, one factor in your advantage is that there's significantly more travel time. But we don't know how strong the case of the employer is. If the employer has to move because of factors outside their control (rental agreement expired, permit not renewed, etc) then they generally have a good case for moving.
In either case, the choice won't be between "accept and resign", it would be between "accept or be dismissed". Do not resign, you would lose Unemployment Benefits and dismissal benefits ("Transitievergoeding")
In the Netherlands, the employer should seek advise from the works/employees council (Ondernemingsraad) that should give an advise. However, the employer is not bound to follow that advise, in which case the council can then go to court.
You should discuss your problems with your employer. You can't force your employer, but your employer is obliged to actively seek a solution with you. If he doesn't even listen to your complaints, it entitles you to ask a judge to terminate your employment and a get severance package and keep your claims to social security.
The way you tell it is that your manager isn't thinking with you at all. Get this in writing! Get everything in writing from now on. Send written recaps of talks that you have to her and if needed to upper management and send yourself a copy to your private email account. (Avoid sending along sensitive company data.)
Possible solutions are that you and your employer can agree upon are for example: partially working from home, have part of your travel time count as working time or that you move to a house near the new office and have your employer pay (some of) the costs. (You said you were planning on moving house anyway!)
In the end, if you can't find a solution, you can always go to court about it. So think about at what phase you might want to consult a lawyer about this.
A lot has to do with how much extra travel time is needed. Dutch jurisprudence seems to see less than 2 hours of round trip travel time normally as not a big issue.