In World War II, the U.S. Navy captured a German submarine off the East Coast. But where in the world was the sub base that posed such an alarming threat to the country?Ruth Patrick became the first female CEO of the Academy of Natural Sciences, which had refused to pay her earlier in her career because she was a woman. (Academy of Natural Sciences of Drexel University)

Military officials didn’t have a clue, but they scraped the crusted gunk off the bottom of the vessel and took it to the Academy of Natural Sciences in Philadelphia, which had an extensive collection of microscopic organisms that live in water. Was there an expert on staff who could take a look?

Yes, there was. Dr. Ruth Patrick, an algae scientist who had excelled in obscurity at the illustrious academy for eight years, was working as a volunteer because no one hired female scientists at the time. She was advised not to wear lipstick to work.

Patrick, who was the world’s foremost expert on microscopic single-celled algae, recognized a particular diatom in the scrapings that lived in the West Indies. Armed with the intel, the military found and destroyed the sub base.

It was a coming out party, of sorts, for the woman who would go on to pioneer the concept that the health of freshwater streams and rivers could be determined by the type and number of organisms living in them. It was a revolutionary idea at the time.

Patrick died in a retirement community near Philadelphia in 2013, not long before her 106th birthday and only a few years after stopping work.

She proved her iconoclastic ecosystem approach to evaluating stream health, now known as the “Patrick Principle,” by spending the summer of 1948 with a team of hand-picked scientists wading into the Conestoga River — then known as Conestoga Creek — in Lancaster County in southeastern Pennsylvania.

It was a time when testing for chemicals was the standard way to search for industrial or sewage pollution in a waterway. But those chemicals may not have been there the day before and could be gone by the next day. Patrick knew of dumping that went on at night so the evidence would be swept away by day.

Ruth Patrick established the concept of using organisms found in a stream or river to determine water quality. (Academy of Natural Sciences of Drexel University)She was sure of her more reliable approach, so she proved it by taking her team into the water at 150 spots on the Conestoga and its tributaries. They looked for leeches, fish, underwater insects, microscopic protozoa, algae, bacteria, nutrients, pH — all things that Patrick believed tell the true tale of stream health.

In 1949, when she published her study, she gave the scientific community a new litmus test for gauging water quality.

“It is a tome. It is amazing. Today, it would be a huge study. In 1948, it was just unprecedented,” recalled Dr. Bern Sweeney, a friend and colleague of Patrick who gave a heartfelt tribute to her in Lancaster in June as part of Lancaster Water Week. “This is the system we’re using today with a few twists. She got it right.”

Patrick’s curiosity in nature was sparked at an early age by her father, an attorney and amateur naturalist who dragged her into the woods each Sunday with a basket that his daughter used to collect anything from the natural world that caught her eye. Back home, Patrick would sit on her father’s lap and peer into a microscope to examine organisms that lived in the creek, invisible to the naked eye. She earned a doctorate in botany from the University of Virginia in 1934.

After the World War II sub discovery, which made headlines, Patrick was finally offered a paying job at the academy. But that same year, in 1945, industrial giants Atlantic Richfield and DuPont approached the academy about using Patrick’s ecosystem approach to look into industrial pollution they had been accused of. Sure, we can do that, but Patrick won’t be leading the project because women can’t manage big projects and big budgets, the executives were told. The executives insisted she would.

She’d do the tests, she told the officials, but the results would be published regardless of what they revealed. If the companies were indeed harming waterways, the public would know.

When she was asked by fellow scientists why she would cooperate with big industry, she would reply, “They need our help.”

Her status growing, Patrick was contacted by the state of Pennsylvania in 1948 to use her system on a stream somewhere in the state to prove that environmental degradation in a stream or river could indeed be ferreted out by looking at its denizens.

Patrick chose the Conestoga and its tributaries because they had a wide range of water quality and could be waded easily for sampling. It wasn’t always clear cut. Some organisms actually thrived in pollution. But Patrick found that a healthy stream had a balance of many organisms with none dominating.

Her team of scientists from many disciplines raised eyebrows both among the local populace and the scientific community as they probed the water. Always at the helm was a woman in printed blouses and a sun hat. Newspaper headlines were along the lines of “Female scientist heads big project.”Dr. Ruth Patrick, fourth from left, poses with her team of scientists who conducted the pioneering study on ecosystem ecology on the Conestoga River in Pennsylvania in 1948. (Academy of Natural Sciences of Drexel University)

“What she included in that study back then is unheard of today,” Sweeney recalled. “We don’t include that many parameters today. You can’t afford to. But she didn’t know what she would get into.”

Patrick became an environmental groundbreaker on a par with Rachel Carson, helping to write the Clean Water Act and winning major environmental awards. She advised President Lyndon B. Johnson on water pollution and President Ronald Reagan on acid rain. In 1996, when she was almost 90, President Bill Clinton presented her with the National Medal of Science, the nation’s highest honor for a scientist. She was one of the first to sound the alarm about global warming.

She also created the Stroud Water Research Center in Pennsylvania, which Sweeney would head for many years. The center conducts freshwater stream research that provides information for Chesapeake Bay restoration efforts. She also created an estuary research lab on the Bay.

After facing years of discrimination for her temerity in a man’s scientific world, she became the first female CEO of the Academy of Natural Sciences that had earlier refused to pay her. She also was the first woman board member and environmental scientist to sit on the board of the DuPont Company.

She continued on at the academy in Philadelphia for nearly 80 years as chair of its limnology department, now named in her honor. She hired a lot of women and was hard on them. At the same time, she taught botany and limnology classes at the University of Pennsylvania for 35 years. Students flocked to be taught by Patrick, even though she was a demanding professor and held mandatory field labs on Sundays.

And she kept expanding the field of freshwater ecology, writing an expansive series of books on the rivers of the United States. Sweeney recalled a field trip Patrick led for a group of industry executives on the Savannah River. Patrick was in her 90s. The executives were gasping. Sweeney flashed a photo of Patrick, wading a stream for analysis at the spry age of 100. She worked five days a week at the academy until she turned 97.

“Ruth paved the way to enable women to excel in science, business and society in general,” Sweeney said. “She had the most difficult road to hoe to become a successful scientist but she became an extremely huge success. She did it through hard work. She was relentless.”

Patrick remained curious until the end. Of anyone she met during a day she would ask what they had learned new in the last 24 hours. Blank stares invited the gentle rebuke, “Then what have you been doing?”