Lobsters breathe through gills, which are located in a structure called the carapace. The carapace is situated at the top of the cephalothorax, which is commonly referred to as the lobster’s head. There are 20 pairs of gills that are separated into two branchial chambers inside the carapace. The gills are made up of short, fine filaments that absorb oxygen directly from the water.
Water enters the lobster’s body through openings on the underside of its body. The water is forced through the branchial chambers by a structure called the gill baler, or bailer. The current of water, which normally flows towards the lobster’s head, can be reversed to clear debris out of the gills and branchial chambers. The flow of water also carries away urine, which contains biochemical signals about the individual’s gender, reproductive state and molting stage.
The gills of the lobster are very sensitive to environmental diseases, such as excretory calcinosis, which causes minerals to accumulate on the gills, according to Wikipedia. This eventually kills the lobster because it blocks oxygen uptake from the water. There was an outbreak of this disease in 2002, in Long Island Sound, that was thought to be caused by warmer water temperatures near the ocean floor, which is the lobster's natural habitat.