potopiti

1. (of a ship) to sink
   Podmornica je potopila neprijateljski brod. — The submarine sank an enemy ship.
2. to flood
   Reka je potopila celo selo. — The river flooded the whole village.
   Komšija nam je potopio kupatilo. — Our neighbour flooded our bathroom.
3. (in liquid) to soak; to dip
   Potopi pasulj u vodu preko noći. — Soak the beans in water overnight.

For a ship going down by itself, potonuti is usually used rather than potopiti se.