This phrase confirms the fact that waves were washing over the sides of the boat, causing it to fill with water. The water makes the boat heavier, which causes it to sink lower into the water. This brings the boat's sides closer to the surface of the water. We know that four of the disciples were fishermen (Simon (Peter), Andrew, James and John; see Mark 1:16–20). They may have been able to swim. The rest of the disciples were unlikely to be able to swim, and therefore there is a serious danger that many of them will drown if the boat is sunk by the waves.
37 And a great windstorm arose, and the waves were breaking into the boat, so that the boat was already filling.