Cut an X, about a half-inch deep, in the top of the pomegranate with a serrated knife.
Fill a 4-quart bowl or pot about 75% full with tap water. Completely submerge the pomegranate and pull it apart into quarters. If this is difficult, try making the 'X' a little deeper, or extend the cuts down the sides of the pomegranate. Once opened, begin to pull out the seeds. The pith will float to the top while the seeds will sink to the bottom.
Remove large pith parts from the water. Discard. Examine seeds and remove any remaining large parts of pith.
Use a strainer to skim off pith and membrane from water surface. Discard.
Take handfuls of seeds and rub them between your two palms to remove any stubborn pith parts. There will likely be some still leftover, but these can be removed once you go to eat the seeds.
Separate the seeds from the water by dumping the contents of the large bowl or pot through a strainer in the sink. Let seeds sit in the strainer set over the bowl for an hour or two to finish draining and drying.
While seeds are draining and drying in the strainer, remove the bad seeds. Bad seeds will be brown in color and soft and mushy to the touch. Discard. You can also skip this sorting process step, and just sort when you go to eat them.
Store pomegranate seeds in an airtight container in the fridge for up to 5 days.