Sample No. 2, Marked from 017 Erie Basin.

Found: Numerous small worms resembling round worms, 0r Nematodes. Numerous diatoms, Oogonia, Conferva filaments, bits of wood, considerable plant epidermis. Ulothrix, Botryococcus braunii, Schizomeris leibleinii, Enteromorpho intestinalis, Grass glumes, Urococcus hookeranius, a. little muscle tissue '(meat), a few spicules, and linen fibres. Sand, argillaceous matter, bits of shell, humus considerable, and a few human hairs.  The sample also contains a small quantity of neutral fat, and fatty acids (soap).

The sample smells very foul, the smell strongly resembling carrion.

Conclusions. This specimen is evidently contaminated with fecal, decaying animal and vegetable matter, wash-water, etc.

Report of the Metropolitan Sewerage Commission of New York, 1910

In 1910, the Metropolitan Sewage Commission produced a detailed, 550-page study of harbor currents, sewage pipe out-flow, water quality and more, and concluded that New York City and neighboring New Jersey needed to "put a stop to unsanitary methods of sewage disposal." 

This massive report, with many photos and tables, noted, among its many points, that the practice of swimming in the water either directly off Brooklyn's piers, or in the floating bathhouses, was unsanitary.  

Included in the report, was a list of the sewers flowing into the waters off Red Hook.

Into Buttermilk Channel........................................ DIAMETER of PIPE.

   Degraw street . . . . . . . . . . . . . . . . . . . . . .  . . . . . . 1 ft. 6 in.
   Degraw street (Gowanus canal flushing tunnel) . . . . . 12 ft. 0 in.
   Hamilton avenue (Old sewer) . . . . . . . . . . . .      . . . . — —
   Sullivan street . . . . . . . . . . . . . . . . . . . . . . . . .. .  . . 1 ft. 3 in.
   Wolcott street . . . . . . . . . . . . . . . . . . . . . . . . .  .. .  . 6 ft. 0 in.
Into Atlantic Basin.
   Bonne street . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . 2 ft. 0 in.
   Commerce street . . . . . . . . . . . . . . . . . . . . . . . . .. . . 2 ft. 0 in.
   Verona street . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 ft. 0 in.
   William street . . . . . . . . . . . . . . . . . . . . . . . . .  . . . . 2 ft. 0 in.
   Clinton street . . . . . . . . . . . . . . . . . . . . . . . . . .. .. . . 2 ft. 0 in.
Into Gowanus Canal.
   Butler street (Greene avenue relief) . . . . . . . . . . . . . 15 ft. 0 in.
   Douglass street (Storm) . . . . . . . . . . . . . . . . . .   . . . . 3 ft. 6 in.
   Degraw street (Storm) . . . . . . . . . . . . . . . . .  . .  . . . . 2 ft. 6 in.
   Sackett street . . . . . . . . . . . . . . . . . . . . . . . .. . . .  . . 1 ft. 6 in.
   President street . . . . . . . . . . . . . . . . . . . . . .  . .  .  . . 1 ft. 6 in.
   Carroll street . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . 3 ft. 6 in.
   Carroll street (Relief) . . . . . . . . . . . . . . . . . .. . . . . . . 4 ft. 0 in.
   Second avenue (Storm) . . . . . . . . . . . . . . . . .. . . . . . . 6 ft. 6 in.
   Nineteenth street . . . . . . . . . . . . . . . . . . . . . . . . .   . . 3 ft. 0 in.
   Hamilton avenue . . . . . . . . . . . . . . . . . . . . . . . . .. .. . 1 ft. 0 in.
   Hicks street slip . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 ft. 6 in.
Into Erie Basin.
   Van Brunt street . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 ft. 6 in.

These sewers are a negative influence on Red Hook's resiliency to floods.

That’s because of 1) the route of the sewer lines and 2) the fact that the City has a combined sewer system.

Regarding 1) the sewer lines (or sewershed) starts up in Park Slope and swoops through Red Hook where a pump then has to push the stuff along the shoreline to the Red Hook Wastewater Treatment Plant in the Brooklyn Navy Yard. That means the sewer lines are very full when they hit the lowlands of Red Hook; and during Sandy, sewer lines backed up into Red Hook buildings. It also means that the pump that is supposed to push the stuff up the coast itself often floods. Then the pump's electrical controls short out, and it stops working. That pumping station is located at the eternal jobsite on the SW corner of Van Brunt and Reed Street on the Van Brunt sidewalk. Conversations with DEP hard hats on site reveal that, in 2017, the DEP intends to move it to higher ground on Reed Street and make it more resilient by putting flood walls around it.

Regarding 2) the water running off the streets goes down a storm drain that merges with the sewer line. Heavy rainwater has nowhere to go, so flooding near storm drains is common in Red Hook when it rains. Heavy rains also means that overflow of combined rainwater and sewage spills into the harbor at the outfall locations (CSOs or "combined sewer overflows").

The full 1910 Metropolitan Sewage Commission report can be read and searched at https://archive.org/details/seweragesewagedi00newyrich 

Compare it to a contemporary study of sewer issues at Open Sewer Atlas NYC. 

The Department of Environmental Protection (DEP) manages all aspects of New York City’s water system (potable water, sewer lines, street storm drains).