“We ourselves feel that what we are doing is just a drop in the ocean. But the ocean would be less because of that missing drop.”
– Mother Teresa
While the government subsidies that most large-scale fishing operations receive are a large part of why sea animals are available for “widespread consumption” and “affordable to the masses,” it is each individual’s choice to eat these animals that keeps commercial fishing operations digging deeper and deeper into our oceans for their next meal ticket.
It‘s Never Enough (“overfishing“)
“By 1989, when about 90 million tons (metric tons) of catch were taken from the ocean, the industry… hit its high-water mark, and yields have declined or stagnated ever since. Fisheries for the most sought-after species, like orange roughy, Chilean sea bass, and bluefin tuna have collapsed. In 2003, a scientific report estimated that industrial fishing had reduced the number of large ocean fish to just 10 percent of their pre-industrial population.“ – National Geographic
Because we have decimated the large ocean fish population, commercial fishing ships are going after smaller species (down the food chain) and going deeper in the ocean.
“This so-called ‘fishing down’ is triggering a chain reaction that is upsetting the ancient and delicate balance of the sea’s biologic system. A study of catch data published in 2006 in the journal Science grimly predicted that if fishing rates continue apace, all the world‘s fisheries will have collapsed by the year 2048.” 
To be clear, our concern is not over the world’s fisheries collapsing, but rather the number of species that are being wiped out for the sake of appetite and our apathy over their plight.
How an aquatic animal gets from the sea to your plate
Most commercial fishing vessels now use state-of-the-art technology to locate and catch aquatic animals. Although it is easy to blame advances in fishing technology for the decline in certain fish populations (and other sea animals), technology is usually created to fulfill a “perceived need” (demand). If the demand disappears, so does the industry and the technology.
A common term used throughout this piece is “by-catch,” which signifies the animals that are inadvertently caught during the fishing process. These animals are thrown back in whatever state they are pulled on board in (i.e. injured, half-dead or dead.)
“Every year across the globe, at least 7.3 million tons of marine life is caught incidentally by fishing.”
Commercial fishing methods
Bottom Trawlers (One of the most common industrial fishing methods)
A bottom trawl is a variety of fishing net that can be pulled along the seafloor. (Remember the satellite pictures of the trawlers leaving a trail of mud behind them?)
Huge (bag shaped) nets are dragged along the ocean floor, scooping up everything in their path. In the most common varieties large metal plates are placed at the end of the net to weigh them down and further rake the ground, stirring up the ocean floor sediment and forcing animals up into the net. Dragging these heavy nets across the seafloor also damages the sensitive sea habitat found there.
They are commonly used to catch shrimp and other bottom-dwelling animals like halibut and sole. In addition to the “targeted animals” they catch, they also produce a catastrophic amount of bycatch. Trapped animals may be imprisoned in the net (with thousands of other animals, rocks and debris for hours on end.) The fish that survive this process may suffer decompression as they are hauled on to the ship (rupturing their swim bladders, pushing their eyes out of their sockets or their esophagi/stomachs out of their mouths.)
When this type of net was first created, they were limited to parts of the ocean that had a soft sediment floor. Now they are used across the oceans and often include huge wheels rigged to the bottom of the trawl to allow it to roll over difficult terrain, subsequently crushing the delicate sea life that is unlucky enough to be its path.
Midwater trawls are used on both small ships and large factory ships. The large ships may use nets up to five football fields in length! They are often large enough to catch an entire school of fish at once as well as any other animals who get in the way.
Unlike bottom trawls they are set high enough that they do not dredge the seafloor. But the animals caught in them may still spend hours trapped in nets with thousands of animals, including the inevitable “bycatch” they produce, before they are hauled on deck.
Think of a drawstring purse made of netting. Purse seines are used to create a large wall of netting which encircles and traps schools of fish. Fishermen then pull the bottom of the netting closed (like a drawstring purse) pushing the fish into the center of the net. This method is often used to catch animals that gather to spawn (like squid) and schooling fish like sardines and tuna. There are a number of different types of purse seines and some versions do catch other animals (such as dolphins.)
When this method is used, fishers may track pods of dolphin (who commonly swim with large fish like tuna). Many of the large fish that this type of net is used to catch such as tuna, cod, and haddock are still conscious when they are hauled onto the deck and their bodies are “processed” (i.e. gills slit or disemboweled.)
Traps and Pots
Traps and pots consist of wire or wood cages that are baited to attract sea animals such as lobsters, crabs, shrimp, sablefish and Pacific cod. The traps and pots are then submerged underwater in areas where these animals are found. The animals are live trapped in the cages, where they wait until the fisherman returns and they are hauled on deck to be frozen, stored or slaughtered on site.
In longlining a central fishing line is used, which can be 50-75+ miles in length. This line is strung with baited hooks (there can be thousands on one line.) The lines are set near the surface (for tuna and swordfish) or laid on the seafloor (to catch cod and halibut.) They are dragged behind the boats or kept afloat overnight. Many of these lines end up hooking and killing sea turtles, sharks, dolphins and seabirds (who go for the bait) along with their intended prey. Some of the animals caught bleed to death, drown or simply struggle against the hooks they are impaled on for hours on end until they are reeled in.
Larger fish like swordfish and yellowfin tuna, due to their weight (up to hundreds of pounds), are notoriously difficult to reel in without the hook ripping out of their bodies. So fishermen use pickaxes and other sharp instruments to impale their bodies in an attempt to drag them on board.
Gillnetting is done by creating a wall of netting in the water (200 feet to over a mile long) using a combination of floats and weights. The net itself is practically invisible to fish and other animals. When a fish attempts to swim through the net (because they can’t see it) they get hung up and when they attempt to back out of the net it catches on their gills or fins, trapping them in the process. This type of net is often used to capture sardines, salmon and cod, but also catches, injures and potentially kills other animals such as sharks and sea turtles.
Fish caught in these nets may suffocate or bleed to death in their struggle to free themselves. Gill nets are often set and left unmonitored so fish and other animals caught in them may suffer for days before being brought to the surface. The fish that do make it onto the ship alive are torn out of the nets by hand and often left to suffocate on deck or are immediately processed (cut open). Fish that were caught in the deep ocean may also endure or even die from decompression. (See the description from bottom trawling.)
Dredging equipment, much like bottom trawling, involves large contraptions that are dragged across the sea floor. But in this case, instead of a weighted net they are made with large, metal-framed baskets. They are used to catch shellfish like oysters, clams and scallops. To force the targeted animals into the metal basket, metal teeth dig into the seafloor, damaging and destroying the delicate habitat and species found there. Like bottom trawling, dredging also produces a large amount of bycatch.
Other methods used to fish not described here include: Seine nets (e.g. beach seine), lift nets and entangling nets, spears, harpoons, pole, troll, cyanide and dynamite.
Slaughter at sea
No matter the method used to catch a sea animal (or otherwise classified sea creature), the animals that are not thrown back (bycatch) after being hooked, caged or netted will either die in the process of being caught, suffocate to death on deck, freeze to death on ice, die as they are “processed” (cut apart) or be “stored” until someone decides to boil them alive or kill them in some other manner for consumption. 90 million tons of carnage a year…and shrinking, but mostly because we couldn’t continue to pull that much life out of the ocean even if we wanted it.
And what about the bycatch?
“…20 percent of shark species are threatened with extinction, primarily as a result of being caught accidentally on longlines.”
“Despite declines in recent years, hundreds of thousands of sea turtles, seabirds and marine mammals, including whales, dolphins and porpoises, die as bycatch. As many as 200,000 loggerhead sea turtles and 50,000 leatherback sea turtles are caught annually. Longline fishing also kills hundreds of thousands of seabirds when they become entangled in driftnets or caught on longline hooks when they dive for bait.” 
Remember that at least 7.3 million tons of marine life (likely an underestimate) are “unintentionally” caught annually. And as you can see from the quotes above, primarily speaking about longlining, many of these animals die from the experience.