I was there a few weeks ago on a layover to catch the KU deal to FRA, I stayed in a place a few blocks from the beach with a nice pool.
After walking around Negombo and seeing the open sewer canals and drains leading to the beach, looking at the color of the sea water and the huge amount of trash littered all over the beach and in the water there was no way in hell I was going in the ocean there although I saw a lot of tourists in my the water, eeeew.

Probably be fine if you stick the the hotel pools.