In 1989, CI began assembly of the Cacapon River ecological baseline with the help of a $25,000 grant from the Samuel Roberts Noble Foundation and substantial financial support from the Cacapon watershed community.  Also at this time, the first issue of Cacapon, the Lab's river journal, was published, and the first Cacapon River bird census recorded 58 species.

By 1990, early baseline data revealed the Cacapon River to be generally healthy, with some polluted "hot spots". Countryside Magazine named Constantz and Ailes to a national list of 20 environmental achievers "who have made a difference". Using the Lab's data, government officials took action against a polluting business.  As a result of CI's success, Constantz left his high school teaching post in 1991 to become full-time Director of the Lab. The Lab won the Sierra Club Seneca Award for Environmental Stewardship, while the Baseline study of the Cacapon continued, and space in a small barn was dedicated for a larger laboratory.  

The year 1992 brought more attention to the institute when the Lab's science-based conservation strategy received broad attention: citizen groups on the Greenbrier and Opequon rivers requested assistance. The Lab won the WV Environmental Council's Mother Jones Award. 

In the same year, the Lab adopted a new mission statement: "Dedicated to using science and education to help concerned citizens protect and restore Appalachian rivers." Working with the Lab, developers and landowners began improving their stewardship of riparian lands. This was also the final year of the Cacapon baseline data collection, and CI began data collection for the baseline of the Greenbrier River.

In 1993, after four years of work, the Lab published Portrait of a River: The Ecological Baseline of the Cacapon River. The response was extraordinary -- almost 2000 copies distributed, local and national media run stories, and requests for copies were received from across the country. The ecological baseline of the Greenbrier River field work continued. The Lab staff designed the "Science with a Smile" program to distribute Cacapon baseline results to all riverbank property owners and improve protection of the river. In the summer, over 250 river lovers attended River Roll On! benefit concert. Also in 1993, Constantz accepted an offer to become West Virginia's first watershed planner, the Lab's new technician, Andy Rogers, began Cacapon tributary water quality survey, and a record number of people -- over 50 -- enjoyed the Lab's five natural history float trips.

The year 1994 began with the Lab researching potential non-point source impacts associated with the rapidly growing poultry industry. Data collection also continued for the Greenbrier River baseline study -- over 60 sites were sampled. Cacapon tributary sampling continued, and the Lab continued lectures for schools, civic organizations, and others.

 By 1995, the second edition of Portrait of a River was published. The Lab and the National Biological Service conducted a joint survey of freshwater mussels in the Cacapon River.  Monitoring continued on the Cacapon, Lost, and North rivers. The Greenbrier River ecological baseline data collection was completed, the Lab held its first open house in celebration of the 10th anniversary of PCREL and over 300 attended. Tributary sampling continued, and Natural History Float Trips continued to expand.

The Lab hired a new Science Director, Neil Gillies, and Bernie Olson was hired to replace Andy Rogers in 1996. The tributary survey was completed, and Cacapon water quality monitoring continued -- five permanent monthly monitoring sites were established. Work began on the Greenbrier River ecological baseline report. The second annual Riverfest was held at Buffalo Gap Community Park. Also in 1996, the Lab held a watershed meeting to discuss voluntary conservation easements.   

In 1997, the Lab moved to a modern facility. Work on the Greenbrier baseline report and Cacapon monitoring programs continued.  The Institute began a new project investigating the impacts of poultry farming on in-stream nutrients in the Lost River; the Lab received widespread recognition for early findings in this study. Using the Lab’s data, the major source of pollution in the Lost River was cleaned up. The third annual Riverfest was held at Camp White Rock in Capon Bridge, and  more than 1000 attended. River float trips and education programs continued.

In 1999 the Institute hired a full time research assistant, Nicole Navis and Education and Outreach Coordinators, husband and wife team Peter and Robin Maille. Research on land use influences on water quality in the Lost River, North River and South Branch of the Potomac continued as the major program, along with the Cacapon River monthly monitoring program. The education program was expanded with help from the West Virginia Stewardship Collaborative.   This year, the Cacapon River Watershed Advisory Council installed watershed signs and ran well water testing program.

Research on land use influences on water quality in the Lost River, North River and South Branch of the Potomac continued in 2000 as the major program, along with the Cacapon River monthly monitoring program. CI began a cooperative project with area farmers, extension agencies, and local businesses to raise eco-friendly Headwater Farms Petite Beef.  In partnership with WVDNR and WVDEP, CI conducted a follow-up benthic macroinvertebrate study and periphyton (algae) studies in partnership with Shepherd College.  We also began computer mapping of land use using GIS (Geographic Information Systems) software, and the website opened for business.

In 2001, the WV Environmental Institute honored  the Headwater Farms partnership with their top award for demonstrating “innovation, creativity, and the ability to think 'outside the box'.”  We were selected because our project was deemed an outstanding model to emphasize the theme of the 2001 Conference on the Environment: “A match made in ‘Almost Heaven.’  In November 2001, the WV Watershed Network praised CI as the group that has “best implemented agricultural land use practices” in pursuit of conservation goals.  Also in November, CI Director Neil Gillies gave a presentation on Marketing Beef Using a Land Stewardship and Clean Water Label  at the Missouri Forage and Grassland Council 2001 Annual Conference.  Research Assistant, Nicole Navis left CI in pursuit of a masters degree in Environmental Science at the University of Wisconsin in Madison.  

In 2002, the USDA-Sustainable Agriculture Research and Education program chose the Headwater Farms program as one of twelve projects (out of more than 200) to profile in their SARE 2002 Annual Report.  The Headwater Farms partners, including CI, were individually honored in Washington DC "for innovative collaboration and good stewardship in developing the Headwater Farms Petite Beef Program."  In May 2002, Neil Gillies gave two presentations at River Networks National River Rally, one on "Partnering with Farmers," the other on using biocriteria to assess streams.  CI completed water quality studies of the Lost and North Rivers for the USFWS.  Final report posted here. 

Funded by National Fish and Wildlife Service Chesapeake Bay Small Watershed Grants Program, the Stream Flow Restoration Project began its pilot project in September 2003.    Began working on Chesapeake Bay issues in West Virginia as member of the WV Potomac Tributary Stakeholder team.  The first Making Science Real Summer Camp (funded by the WV Department of Education) was held in July, and the first Stream Scholars Summer Camp was held in August.  Eight students from partner schools in Grant, Hardy, and Hampshire Counties participated in the three day non-residential camp for 7th to 9th graders.  The goals of the Stream Scholars camp were to promote environmental leadership, increase college enrollment in West Virginia, and increase student interest in environmental careers.  The camp was made possible with support from US EPA, MARPAT Foundation, CI members and partner schools.  In late December CI hired its first membership coordinator, Claire Pitner.        

The Stream Flow Restoration Project  continued in 2004, along with the two summer camp programs. That year, CI received grants from USEPA and Canaan Valley Institute to build an internet based environmental school.  Continued  working on Chesapeake Bay issues in West Virginia as member of the WV Potomac Tributary Stakeholder team; receive contract to serve as primary author of Tributary Strategy document.  Monthly Cacapon River water quality monitoring continued, and we began to investigate revisiting the Cacapon baseline study.

 In 2005, CI opened the Potomac Highlands Watershed School, our internet-based environmental school.  Hold first PHWS Environmental Forum on deer overpopulation issues.    In addition to continuing our Stream Flow Restoration Project , began Revisit the Baseline study, and continued Cacapon monitoring project.  Cooperative project studying effect of improving water quality on a wild rainbow trout stream.  we ran Stream Scholars Summer Camp for a third year, including 2-day trip to the Chesapeake Bay.  Continued  working on Chesapeake Bay issues in West Virginia as member of the WV Potomac Tributary Stakeholder team, beginning work on implementation of tributary strategy - including oversight and monitoring of two riparian buffer demonstration projects.  Began work on Lost River Watershed Based Plan.

CI developed its first ever strategic plan in 2006, and in the process decided to update its mission statement to: From the Cacapon to the Potomac to the Chesapeake Bay, we protect rivers and watersheds using science and education.  Hired new Education/Outreach director Frank Rodgers.  Continued  working on Chesapeake Bay issues in West Virginia as member of the WV Potomac Tributary Implementation Team.  Continued Stream Flow Restoration Project , began Revisit the Baseline study, and continued Cacapon monitoring project.  Cooperative project studying effect of improving water quality on a wild rainbow trout stream.  Continue work on Lost River Watershed Based Plan projects.  Continue operating internet-based the Potomac Highlands Watershed School.  Hold two PHWS Environmental Forums: Stream Cleaner Environmental Forum modeling the effort to cleanup the Chesapeake Bay; and Oh Deer! Environmental Forum on deer overpopulation issues.