Ships routinely discharged their wastes overboard. By that, I mean that if you flushed a toilet, what you flushed went through the sewage lines and out a discharge set just above the waterline. For all I know, it may still be that way.
But when people began to become concerned about pollution, attention inevitably turned to the Navy's ships, which were sitting at anchor or tied up to the pier and discharging raw sewage into the harbors and coastal waterways. That had to stop. The first thing that happened was that the piers were outfitted with sewage lines. The ships were re-piped so that instead of simply discharging sewage over the side, ships in port would pump their waste to the pier lines. This was not so simple, as the pier discharge lines were higher up than the overboard discharge ports, so that sewage pumps had to be fitted to some ships.
Then came the issue of transiting coastal waters. Ships were fitted with tanks, called CHT tanks. CHT stood for, depending on whom you asked "collection, holding and transfer" or "contaminated holding and treatment". The tanks were sized to hold several hours worth of waste. The hammer for making sure that the tanks were used was that the captains and chief engineers could be held personally responsible by the Coast Guard for any discharge of untreated wastes. And some poor saps did have to pay the fines.
After a ship cleared coastal waters, the sewage drains would be aligned to go back overboard and the CHT tanks were flushed out and pumped out. The navigator was responsible for determining when the ship was far enough out to sea. Of course, it wasn't the navigator who had to pay the fine if the word to cut the sanitary drains overboard was given too early.
When the Navy began to send ships on goodwill cruises along the Great Lakes, some people noticed at first that it was almost always the same ships that were sent. That was because those ships had to have greatly increased CHT capacity in order to hold their wastes for the time it took to steam from one port to another.
The sewage system and the CHT tanks were maintained by the HTs, which earned them the nickname "shitter techs". The CHT pumps could be a nightmare and if they failed, then raw sewage backed up into the shower drains in the heads that were on the low points of the system. And that would make the XO very, very cranky.
 The fines were about $25,000 per incident.
 Paying them off at $250 a month for a hundred months sort of put a crimp in one's cash flow.
 A by-product of the requirement to not pump wastes overboard in port was that the age-old practice of using anchorages in home port came to an end.
 They also needed permission from the Canadian government, as the Great lakes were demilitarized under the Rush-Bagot Treaty of 1818.
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