Hi Aeron - sorry to hear about your problem. I don't know if we have anyone here who is familiar with law in the Philippines and we are primary a United States based law forum. Your question does cover an area of law that I would be surprised if it was much different in your country. There are also questions where water runs through land and flows from higher ground to lower - and I'm not sure if that is the type of question you're asking. This body of law here is known as "Riparian Water Rights."
From my understanding, the neighbor doesn't even have a right to interfere with the area that is crossing into your land - so the logical answer is "no." You'll probably need someone locally to advise you on the law. In most places, sending a certified demand letter (such as a demand to cease and desist from what they are doing" is usually the first step. If you go to court, you'd need to show the court that you gave the defendant notice of the issue, they knew about it and refused to comply. Best of luck with your issue.