Slowly Sinking

How much of the rest of the system is below water - if it is leaking only when the engine is not running, and when the seacock is open, then would have thought it must be on the inlet side, and on something which is below sea level. Perhaps from the front of the water pump?

Does it happen when you are sitting in harbour or just whilst you are underway?

Could there be something odd going on with the shaft seal - what sort of seal do you have? A grease seal will leak when turning, but a lip seal type could leak only when under power.
 
Have you looked at the water pump. My Yanmar loves to drip from the water pump. A small amount of water appears, rusts the oil pipes below the pump and collects under the engine.

For the genuine Yanmar replacement of water pump shaft (gets grooves from silt in it) and the water/oil seals, expect to pay £70-90 for the parts. I need to replace the shaft every 300 engine hours or so here in the Hamble . I also visit Lymington which uses a special kind of grinding paste to float boats in. It is kept well mixed in by the ferries.
 
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