The Flower Garden Banks sit atop several salt domes near the edge of the continental shelf about 100 miles from the Texas and Louisiana coasts. The domes, which rise several hundred feet from the seafloor, are topped with corals, algae, sponges and fish, and each bank is separated by miles of open ocean, Rice describes.
It is the only national marine sanctuary in the Gulf of Mexico.
The sanctuary is also expanding, nearly tripling in size. The addition of 14 reefs and banks to the three already included enlarges the sanctuary from 56 to 160 square miles, the National Oceanic and Atmospheric Administration said.
Marine biologist Adrienne Correa, who co-authored the study in Frontiers in Marine Science, said experts were shocked to see the reef was affected.
"One thing we always thought the Flower Garden Banks were safe from was terrestrial runoff and nutrient pollution. It's a jolt to realize that in these extreme events, it's not just the salt marsh or the seagrass that we need to worry about. Offshore ecosystems can be affected too."
Correa and her colleagues sampled sponges at the sanctuary for three consecutive years: 2016, 2017 and 2018. Samples collected after the extreme flooding in 2016 and 2017 contained E. coli and other human fecal bacteria. E. coli on sponges in 2017 came from Harvey floodwaters.
While many studies have shown that nearshore reefs can be harmed by pollutants washed into the ocean by rainfall over land, marine biologists generally assume ecosystems far from shore are safe from those dangers.
But as lead author Amanda Shore found, "This shows perhaps they aren't protected from severe events. And these events are increasing in frequency and intensity with climate change."
Houstonians know flooding events all too well.
In April 2016's Tax Day flood, a severe storm dropped more than 17 inches of rain in some places in less than 24 hours. Sadly, three months after the storm, recreational divers reported murky waters and dead and dying organisms at East Flower Garden Bank.
WATCH: Compelling images and your stories from 2016's historic Tax Day flooding
Harvey dropped an estimated 13 trillion gallons of rain over southeast Texas in August 2017. The storm is recorded as the most intense rainfall event in U.S. history.
Interestingly, marine biologists found the reefs fared better after Harvey than in 2016 because of the ocean currents.
"Instead of going straight out from Galveston Bay and over the Flower Garden Banks, the water ended up turning a bit and going down the Texas coast instead," Shore said.
Still, that doesn't mean there was no impact at all from Harvey on the reefs.
Rice's study found that research buoys measured a 10% drop in salinity in less than a day on Sept. 28.
Correa's team also found genetic evidence that fecal pollution gathered from the banks in October originated in Harvey floodwaters in Houston.
Follow this link to read Rice University's study in its entirety.
More about the Flower Garden Banks National Marine Sanctuary
The largest addition to Flower Garden Banks is called Horseshoe Bank, because of its shape. It's 121 miles south of the Texas-Louisiana state line, between the sanctuary's two original banks. At 28.7 square miles, it's also the second-largest of the 17 protected areas in the Gulf.
Horseshoe Bank is made up of thousands of "patch reefs" where corals, sponges, algae, invertebrates and fish are found, according to NOAA. The area also includes a few mud volcanoes, NOAA said on the sanctuary website.
The East and West Flower Garden Banks made up the entire sanctuary when it was created in 1992. NOAA found Horseshoe Bank when it mapped the area in 2004.
West Flower Garden Bank, the sanctuary's largest, covers 37.2 square miles. Horseshoe Bank is slightly larger than East Flower Garden Bank. The smallest on the list is Stetson Bank, a 1.4-square-mile area off Texas that was added to the sanctuary in 1996.
All of the other additions are dotted off Louisiana's coast, with the two easternmost, Parker and Alderdice banks, south of Iberia Parish. The additions range from 2 square miles to 11.5 square miles.
Alderdice Bank includes "three spectacular basalt spires" about 60 feet tall, according to NOAA. They are about 77 million years old, making them the oldest known exposed rocks on the continental shelf along Texas and Louisiana, the website says.
Parker Bank includes significant habitat in the "twilight" area between waters considered deep and shallow. Black corals, octocorals, fish, sponges, algae and invertebrates are found on it.
The Associated Press contributed to this report.