As a group of researchers floated down the Penobscot River, they took note of the evident changes in one of Maine’s most cherished and historied waterways. Above the old Veazie Dam site, the end of a boat ramp hung several feet above the river’s surface. Boom islands, built of cobble and timber, had resurfaced after decades underwater. And the rafting guides craned their necks, searching for recently formed hydraulics.

Since the removal of the Great Works Dam in 2012 and Veazie Dam in 2013, people have watched the lower Penobscot take a new shape, some with more interest than others.

“Look at that beautiful esker,” said Sam Roy, a Ph.D. student at the University of Maine School of Earth and Climate Sciences. On a laminated U.S. Geological Survey map, he traced the contours of a glacial deposit with his finger down the west banks of the Stillwater and Penobscot rivers.

Roy was one of several UMaine students invited on a Friday rafting trip down the Penobscot to study the riverbed with sonar technology. Led by two Maine Rafting Expeditions guides, the group began its journey in Old Town, just below the Milford Dam. After piling into two whitewater rafts, professors and students juggled paddles and sonar equipment as they floated downstream.

“Primarily, we’re interested in the structure of the bottom of the Penobscot River and the changes to that bottom as a result of everything that’s gone on, including human interventions, floods, dam removals and all the other things that have been a part of the history of the river in the last 200 years,” said Sean Smith, assistant professor at UMaine’s School of Earth and Climate Sciences.

A fluvial geomorphologist, Smith is devoted to understanding streams and rivers. For several years, he’s been interested in researching the Penobscot River, which is the largest river system in the state, stretching 109 miles from its headwaters in northern Maine to the ocean.

“The bottom line is, you can’t manage any river effectively unless you know how it works and responds to direct and indirect influences of geology, climate and humans,” Smith said.

Soon after launching, the rafts encountered rapids below the Milford Dam.

“You’ll want to stow away things you don’t want to get wet,” warned rafting guide Arthur Dickey as he steered toward the frothing waves ahead.

While for a scientist, a changing river could mean new habitat for wildlife and an opportunity to test new technologies, for a whitewater paddler, a shift in a river could mean a new and exciting run. That’s the case for Dickey, owner of Maine Rafting Expeditions.

“There’s a lot more water here than I was expecting,” Dickey said, pointing out a “fun hydraulic” that he’d have to remember for his next trip down the river.

After the whitewater, the group set down the paddles to set up the equipment that would map the bottom of the river with sonar.

“Our interest in the bottom is for what it means to the fish,” said Gayle Zydlewski, associate professor at the UMaine School of Marine Science.

Zydlewski is studying sturgeon, a large primitive-looking fish that moves along the river bottom, disturbing substrate to feed on plants and animals.

The Penobscot River historically supported spawning populations of both the endangered shortnose sturgeon and the Atlantic sturgeon, according to the Penobscot River Restoration Trust.

“Sturgeon would get as far as the Milford Dam, and when the dams went in, they were blocked,” Zydlewski said. “And so, now that this area is opened up, we’re interested to know, will they use it? And will it make a change to their population?”

Restoring various species of sea-run fish to the river is one of the major goals of the Penobscot River Restoration Project, which is an unprecedented collaboration between the Penobscot Indian Nation, seven conservation groups, two hydropower companies, and state and federal agencies.

“They’re trying to use it in managing fish populations,” Zydlewski said. “So we try, as we’re collecting data, to give them as much information as possible, even before it’s fully analyzed, so that they can make wise decisions about moving fish or permitting decisions.”

Since spring 2006, UMaine researchers have documented more than 400 shortnose sturgeon in the Penobscot, the first confirmed captures since 1978. In addition, close to 80 Atlantic sturgeon have been caught and released. Under a NOAA-Fisheries Endangered Species permit, all have been tagged for later identification to estimate population size. And a number of the sturgeon have been tagged with ultrasonic tags, which are used to determine migratory patterns and habitat use in the river.

Aboard the raft, Zydlewski searched for sections of the river with the potential become sturgeon spawning habitat in the future.

“In other rivers that sturgeon will typically spawn in cobble boulder type habitats,” Zydlewski said. “Sturgeon has very sticky eggs so they stick to whatever surface they can attach to.”

The equipment setup for the day included a Humminbird fish finder, a GPS device, a GoPro camera and a small flashlight, all ziptied to a “T” built out of PVC pipe.

“We’re trying to set this up so it’s inexpensive and portable,” Smith said.

“One of the hardest things to do in a raging river is measure something accurately,” Smith said, “but with the advent of modern technology for sonar and computering, you can use devices that are much smaller than they used to be. So we’re experimenting with some of these devices.”

“We’re sending a sound down to the bottom, and depending on what it bounces off of, we might get a signal back that tells us whether its sand or cobble or bedrock. And actually, we’ve used this same thing to look for fish,” Zydlewski said.

In addition, the GoPro camera, which was placed underwater at the end of a PVC pipe, took photos of the river bottom every 10 seconds as the raft floated downstream.

“For the future, what we hope is that we can repetitively run down a river or stream in a raft — or a paddleboard even — and do this,” Smith said. “It’s a work in progress.”

In the other raft, Cory Gardner, a research technician, held a radio receiver above the water, listening for tagged salmon and shad.

“It’s an amazing laboratory for the university to conduct research and set up student experiences,” Smith said. “It’s funny to me that the community I’ve most often seen on the river is associated with research, and the individuals always seem to enjoy their time on it. Maybe it will take a while before the larger community realizes how cool it is that [the lower Penobscot] is now open to navigation.”

As the rafts approached the old Veazie Dam site, Dickey pointed out a juvenile bald eagle perched on a crumbling boom island, a structure of lumber and cobblestone that was used by river drivers to sort logs as they moved downstream. Many of these old structures emerged when the water dropped after the removal of the Veazie Dam in 2013.

The data gathered during the four-hour trip, which ended in Brewer, will be compared with studies conducted before the dam removals, as well as data collected on future trips down river, to ascertain how the lower Penobscot has changed — and will continue to change — now that it’s flowing freely.

To learn about the Penobscot River Restoration Project, visit

Aislinn Sarnacki

Aislinn Sarnacki is a Maine outdoors writer and the author of three Maine hiking guidebooks including “Family Friendly Hikes in Maine.” Find her on Twitter and Facebook @1minhikegirl. You can also...