Do you mean lots of little tiny bubbbles? Did you bleed your system enough? Sometimes tapping the tubes will get the bubbles flowing. But once they get to the res, they should go to the top and pop. What kind of coolant are you using?
Thousands, no millions, of micro-bubbles. The fluid and bubbles are moving along nicely. Using clear PrimoChill coolant. The clear tubes are opaque. Actually, it's so sudsy it's like foam. Yes, I did bleed the system. The rad has a bleed hole at the top.
Not bleeding all the air out will cause bubbles.
A small leak could let air in. "Less likely"
Is it an after market cooler or custom made?
I havent tried water yet, but I've been researching it and I think you need a radiator and a seperate reservoir to keep all the air out. Without the reservoir when you get evaporation you could get air.
Hopefuly its not bubbling because its boiling the water from being to hot. That would suck.
Im guessing you got in a hurry and didnt bleed it right. Sometimes you think you got it and there is a pocket of air hiding that shows up later.
It actually took a couple days to get all the coolent bubbles out of my system. Just let it run, it shouldn't be filled to the max it should have a little space in the top of the resevoir. The instructions for my unit said to leave aproximently 1/2" of space empty in the resevoir. As the bubble work thru the system they will pop in the open space and filter out of the system.