Should one resign from working on a water treatment plant project that is feared to fail due to practices aimed at profit at the expense of project quality, or should one continue while absolving oneself of blame by reporting the risks?

If you know that the station's design will be used for financial manipulation, then it is not permissible for you to participate in it, as that would be assisting in sin. However, if you did not know about this until after the design was completed, then there is no blame upon you for continuing to work, provided that you offer advice to the officials capable of preventing corruption, and that you do not assist those engaged in manipulation. If you fear great harm, then resignation is preferable.