Pollution became a major problem because of Buffalo's prominence as an industrial center. Factories near the river and lake discharged wastes right into the water, and surrounding communities did likewise. By the turn of the century, the Buffalo River was considered not fit for drinking water or fish. The Niagara River, with its deep waters and swift currents, broke up concentrations of pollutants, but a lot still got into the river. As early as 1893 a writer for the Buffalo Morning Express said that, thanks to the construction of several sewage lines that led directly to the river, the fishing was not what it once was. The 1930s saw major fish kills in the Niagara River. There was some improvement in the 1930s when the first sewage treatment plants were built, but heavy rains and spring melt-off often would overwhelm them. In 1940 and 1941 there were discussions on how to improve local fisheries and clean up the lake. But with the outbreak of World War II, these good intentions were put on hold for the duration. Factories were soon running full blast to aid the war effort and concerns about pollution took a back seat to defeating the Axis Powers.

The Depression years hurt the local fishing communities, although many people saw fish as a free food that could stretch the family eating dollars. Also, extra fish could be sold at the dock. The fishing communities became dilapidated. New arrivals often were people who had lost their homes and were looking for inexpensive places to live. Some might have been considered middle class a few years earlier.

Some local politicians called the Towpath and Marsh "eyesores" and vowed to have them razed and the residents evicted. They were successful in clearing out squatters who lived in abandoned canal boats and in a smaller community near the foot of Georgia Street, but had little success in ousting the Towpath and Marsh neighborhoods.

The Erie Canal, once so busy, was abandoned in 1918. It was polluted and considered a menace to safety in the 1920s and '30s. In Black Rock and Riverside, swift currents resulted in drownings of several children. In the 1930s, the canal was filled in between Buffalo and Tonawanda, part of a WPA project. It was not fully complete until after the end of World War II.

The war years brought major changes for local fishermen. Since Buffalo was a major industrial and transportation center, and had several shipyards where vessels for the Army and Navy were being built, security around the waterfront was very tight. Anyone who worked on the waterfront or had recreational interests had to obtain a pass, which involved paperwork and being fingerprinted and photographed. Armed guardsmen patrolled the waterfront to enforce the rules. This rule remained in force until October 1944.

Also at the foot of South Michigan Street, the Great Lakes Liners SEEANDBEE and the GREATER BUFFALO were being converted into aircraft carriers, the world's only steam-powered, side-paddle wheel aircraft carrier, to be used to train aircraft carrier pilots on Lake Michigan. While the conversion work was underway, the waterfront was off limits to everyone except those working on the ships, or those who had passes issued by the U.S. Coast Guard.

Commercial fishing activity, which had been in decline since since the collapse of the herring fishery, intensified during the war years. Unlike meat, fish were not rationed, although prices were regulated. This put more strain on already stressed populations of fish such as blue pike, yellow pike and whitefish.

In 1945, there were no more restrictions on the waterfront, but there were changes. Outboard motors were seen on more and more small boats, and the graceful rowing boats began to disappear. Even the materials used to build boats changed. Fiberglass and aluminum would make their debuts, eventually replacing wooden boats entirely.

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