How is your cockpit drained? On my boat the 2 drains have short runs of hose run to the stern. I just replaced one of them because of chafe that would have eventually allowed the hose to leak into the bilge instead have the water flow into the ocean.
Also, if this happens again (I hope it dosn't), try to check the water before pumping it overboard. Seawater smells different than freshwater or contents from your holding tank. After I made sure it's not the (wastewater-) holdingtank, I would actually taste a minute amount to figure out whether it is seawater or freshwater.
Make sure to make your floatswitch highest priority. Even a very small leak can sink your boat in the slip within a couple of days!
Hope you find the source soon.
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Island Packet 37 (hull53)