JACKSONVILLE, Fla. – The St. Johns Riverkeeper group filed a petition Friday against the state Department of Environmental Protection over the proposed dredging of the St. Johns River.

The Jacksonville Port Authority and the U.S. Army Corps of Engineers are planning to dredge the river to be able to accommodate larger ships and compete with other ports.

In February, the DEP issued a permit to allow the corps to dredge 13 miles of the St. Johns River from the mouth of the river to Brills Cut, which is near the JaxPort Blount Island terminal.

But the St. Johns Riverkeeper says dredging to a depth of 40-51 feet will have "devastating long term effects" on the river and several endangered species.

"Simply put, this permit fails to protect one of our state’s most important natural assets – the St. Johns River,” said Lisa Rinaman with St. Johns Riverkeeper. “Once the damage is done, there is no turning back. We simply cannot afford to get this decision wrong."

DOCUMENT: Riverkeeper's lawsuit challenging dredging

The St. Johns Riverkeeper told News4Jax the plan does not protect the river enough from the damage the dredging would cause. They hope through the petition, they can find a compromise that's better for the river.

Rinaman emphasized the river could look much different if the current plan to dredge it goes forward.

"It's our job to protect the St. Johns River," she said. "And the dredging plan, as it currently is written, does not do that."

The project would be an eight-year process during which time the St. Johns Riverkeeper says dredging would cause the water to be more cloudy, change the salinity and make the river more prone to algae blooms.

"We have historically dredged our river for many years, and every time it's deepened you see more salt water intrusion and so as you get more salt water into our estuary it upsets that delicate balance. So it does damage to our wetlands and to our grasses, which are the kidneys (of) the St. Johns River, and that damage will be (due) to more water quality issues which will basically limit our ability to enjoy the St. Johns," Rinaman said.

Once the bigger cargo ships start coming through, the environmental organization claims there will be an increase in shoreline erosion. Before the dredging starts, explosives and hydro-hammers would be used to break up the rocks on the river bed for 250 days, which the Riverkeeper group says will have its own harmful effect.

Nancy Rubin with JaxPort says the agency wants to protect the river too and work to find a middle ground to protect a vital resource for many years to come.

"We have worked for several years as a group to have this be a win-win for everyone, to make sure that the dual priorities of protecting our natural resources and growing jobs and dollars for the people of the region can continue a pace, can work together and we will continue to do that," Rubin said.

The St. Johns Riverkeeper told News4Jax if some kind of agreement cannot be reached through the petition, it plans to do a federal challenge of the Army Corps of Engineers plan.

News4Jax reached out to the corps and a spokesperson said it stands by the DEP.