Generally water only gets in at seals, where moving panels fit, or external bits are fitted. Or where sealing plugs are displaced. Occasionally seams leak, but this is rare.
First, is the water clean or dirty?
Clean indicates rain. Possibly hatch seal or rear lamps. May be aerial if at the back of the roof, but you'd usually get a wet rooflining first. You could try or consider any or all of the following.
Does the rear hatch fit properly? Put talcum powder on the sealing edge of the seal and close the door against it gently. Open it again and check it has met the seal properly all around. Leave the talc there, it will show traces if water leaks past.
Remove the trunk carpet and wheel. Sprinkle talc around the edge of the wheel well. This will show from where the water is arriving.
With the carpet out, run water over the rear lamps and see if it arrives in the trunk. May need to shut yourself inside, while a helper pours the water on. If the rear lamps are not sealing, remove the seals and turn them over. You effectively get a new seal.
Dirty is thrown up from the wheels. Look for missing plugs.