We have strainers for the engine and generator intakes that are directly above our Maralon seacocks. The top of our main engine and generator strainers (with the cover removed) is near the natural waterline (but, just below it).

For us, it's the generator that gets clogged. We almost never run the main engine, unless we're moving the boat; and, we haven't had a problem with clogging.

In the case of the clogged generators, unless it's been nettles in the Chesapeake, we have had eel grass in Newport, Martha's Vineyard, Nantucket, and once in Block Island.

For eel grass, we've been able to take a VERY long giant plastic wire tie (like 3/8" wide and 2' long) and worked the opening from above like a plumber's snake. That usually cleared the intake of our generator of eel grass. Once, in Newport Harbor, we sucked-up a "mass" against the through hull. I cleared that by running the prop in forward and reverse quickly, and alternately, while at a mooring (looked stupid, had to be careful, etc.). The mass was flushed away. The few strands then were cleaned-up and we were good to go for a while.

I learned that unless you have a few spare impellers and know how the change them, you'll be sorry! (I found a supplier on a Saturday afternoon, took a very expensive cab ride to Jamestown Island and back to Newport, and bought 3 generator impellers. Now I have a bunch on the boat for both the main engine and the generator.

The solution that Greg suggests looks pretty neat! I'm going to see about getting me one of those!