Navy Blue '90, just like its predecessor, uses the classic Battleship playing principle: two players place ships on a 8x8 grid and then, in turns, guess a position on the opponent's grid. The goal is to hit all ship parts first. There are a few extra weapons available which allow to scout enemy grids or hit multiple grids at once.

The main difference to the predecessor is that players have to choose their equipment before the match starts: three ships (out of seven) and which/how many extra weapons. There is also a time limit in place which restricts the time to choose the next move.