Most sea water pumps inlets should have been installed BELOW the actual water line (AWL) of your boat and all those inlet lines too.
If opening the inlet stainers allows water to flow into your boat, then they are below the AWL.
Trace the line from those strainers to they pump inlets (suction). If those lines are alway below the AWL, then you should have a flooded pump.
Last...
If all of the above stuff is below the AWL, then your pumps are NOT free to flow, as designed. I assume those devices are discharge ABOVE the AWL or out into the air.
So...
If your equipment ALWAYS did this, then you have a "seal trap". What is that? Look under your kitchen sink that has a "U Trap, Seal Trap, P Trap". That TRAP prevents sewer gas from escaping into your house. Just like the Air TRAPED in your boat systems.
My Guess...
Since you have 2 systems not working well my guess this is NOT true...
Then each system runs fine
but they are BARELY working.
My AC was cutting on and off. I was about to call a Tech. Neighbor boat owner told me, "I can fix it!" and he did. There was water discharging, too. I thought is was FINE.
He closed the sea cock, took off the discharge hose, brought a "As Seen on TV" flex hose with a shut off valve and a tapered tip. He jammed that tip into the hose, turned on Dock water pressure and about a ton of algae and crap blew out the over board discharge. We purged it for about 3 minutes or until it was clear water. He reassembled the system, opened the sea cock, and now a major change it the flow of water. My AC got cooler and stopped the cycling since it was at high temperature cut off.
I do this now annually.
Take Care
Jim...