Make videos of his actions both toward you and your family and the dumping of sewage in the sea. Make sure they are date stamped.
Find, if you can, others who are willing to speak out about this clown. Maybe a PI to investigate who he is and his background.
If your property is
surveyed make sure you have copies to prove what is your wife's land.
File complaints with the Department of Natural resources for his polluting and encroachment of the area near the beach where it is not legal to build.
Chan Robles on line law is a great source of legal info.
https://chanrobles.com/
File a complaint with the NBI if you are able.
Call the 8888 hotline and report his actions, his building on the beach and polluting the ocean.
In other words, gather all the evidence you can against this clown and report him to any and all Govt. agencies who will accept the complaint.
Hire an attorney to work with you and your wife in dealing with the rogue barangay captain.
If your wife is friends with the Mayor, make use of that.
This guy might just be a poor man trying to make a home for his family as someone stated, though he is first and foremost (according to your comments) a bully and a first class asshole.
Use your head and your time and all the resources you can find and gather to your side.
It may be slower than just taking him out, though the sooner you get started the sooner you'll see results.
If you've already done all this, Nevermind