City, county and state continue efforts to improve Naples Bay

Karl Schneider
Naples Daily News

Naples Bay has suffered from increased flows of fresh water and pollution since development and canals cut through its mangrove-lined shores.

A 20-year plan to clean the bay would've been halfway done this year but was quietly abandoned. Yet the city, county and state continue to work toward restoring the bay.

The City of Naples' natural resources division earlier this week presented a water quality report on the bay outlining the current problems, success stories and potential solutions.

For decades, local agencies have tried a plethora of efforts to bring the bay’s ecosystems back to a more natural state, yet it remains impaired.

Scientists have identified fresh water flows from nearby creeks and lakes as a source of impairment. The bay, along with those fresh waters, all suffer from copper and bacterial issues as well as too much chlorophyll, nitrogen and phosphorus, according to a presentation given to the City of Naples on Monday. 

Stephanie Molloy, the city’s natural resources director, along with Cardno senior scientist Ed Call, presented a report to identify areas for improvement and focus on what has been working. Cardno is a professional service specializing in physical and social environments, according to its website.

Restoration efforts have been focused on the bay’s oyster populations, seagrass beds and mangroves.

Houses line the shore of Naples Bay on Thursday, August 6, 2020. As the area's population has expanded over the past few decades, bringing increased development and the building of canals, an excess of freshwater has been flowing into Naples Bay causing an influx of nutrients and pollutants that are damaging to the bay's ecosystem.

The bay has lost 80% of its oysters in the past 60 or 70 years, said Katie Laakkonen, an environmental specialist with the City of Naples. Oysters are a natural water filter and hundreds of different organisms depend on oyster reefs. She calls them “mini-condominiums.”

The city’s oyster reef restoration project built artificial reefs at  three separate sites and staff is continuing to watch the success of the program and the increasing number of oysters on the reefs, Molloy said.

“The three main goals are to improve water quality, improve the habitat and the physical structure of reefs,” she said. “This will help protect shorelines from storm surge, boat wake and sea-level rise.”

More:Naples seeks public input on water quality improvements to city lakes

It’s estimated that 90% of the bay’s seagrass has been lost since the 1940s, Laakkonen said. These plants can help stabilize sediment and keep shorelines from eroding, she said. City efforts are focused on monitoring the southern portion of the bay. 

Seagrass is susceptible to the wavering salinity of the bay and during the dry season, when freshwater inputs are reduced, seagrass has been spotted in some upper regions of the bay.

Mangroves, like seagrass, act as a nursery for a variety of marine life. Only about 30% of the original mangrove habitat remains along the bay, Molloy said.

“We’re not going to get Naples back to where it originally was, so our goals are to improve what we can where we can,” she said. “We’re aiming to maintain and improve the mangroves that we currently have and any areas where we can add mangroves, we would like to do that.”

(The channelization surrounding Naples Bay has extended its perimeter from 46 kilometres to 102 kilometres. The images shift from the 1927 shoreline, to 1965 and finally to the 1978 shoreline. Source: Mike Bauer. GIF creation: Alex Driehaus.)

Molloy and the natural resources division presented a separate agenda item Monday suggesting council members ask the Florida Department of Environment Protection to cede regulatory powers of mangrove trimming and cutting to the city.

Molloy said the DEP rarely denies permits to trim or cut mangroves, and this would give the city the ability to curb the tree’s removal.

Naples’ mayor and city council seem primed to make progress in efforts to restore the bay.

“We don’t want to do small efforts,” Mayor Teresa Heitmann said. “We’re really looking at larger mitigation pieces. It is all about coordination and communication.”

More:Burmese python caught while swimming in Naples Bay

In 2010, Mike Bauer, former director of the city’s natural resources department, put together a 20-year plan to restore oyster populations, seagrass beds and mangroves in the bay. The plan was the first major capital project from the city to improve the bay, he said.

“(The 20-year plan) had a very good reception when it was introduced,” Bauer said. “City council was excited about it.”

The plan has since been abandoned, but Gregg Strakaluse, director of the City of Naples’ streets and stormwater department, wrote in an email to the Daily News that the city’s 2018 stormwater master plan is “embracing (its) optimism and spirit.”

Bauer presented a five-year update in 2015 acknowledging the 20-year plan would require significantly much more time, effort and resources, Strakaluse wrote.

“The City’s Stormwater Master Plan contains specific projects and programs that have technical merit for success, not just for Naples Bay, but also for Moorings Bay and the Gulf of Mexico,” Strakaluse wrote.

The updated stormwater plan included $60 million of projects and programs meant to be taken on in the next 10 years, he wrote. These do not, however, include efforts by Collier County and the Big Cypress Basin.

The basin, a subsection of the South Florida Water Management District, manages just under 150 miles of canals in Collier and part of Monroe County.

Lisa Koehler, the basin’s administrator, laid out the problems surrounding Naples Bay in simple terms: there is no one silver bullet that will restore the bay.

The basin has worked on four projects over the years to help curb the nutrients flowing from freshwater sources into the bay.

More:Naples Council votes to spend $1 million to improve Naples Bay water quality

  • It worked with the City of Naples to clean up flows from Lake Manor by dredging and increasing plantings around its shoreline to help soak up nutrients.
  • The basin and the Conservancy of Southwest Florida worked on a filter marsh on the conservancy’s property. The marsh captures water and improves water quality as it absorbs nutrients before it re-enters the bay’s watershed.
  • In conjunction with Collier County, the basin developed Freedom Park as a greenspace. The park acts as a filter before freshwater from surrounding neighborhoods is diverted from the park and into the bay.
  • A second partnership with the county provided stormwater improvements west of Goodlette-Frank Road to absorb more nutrients before runoff landed in the bay.

Curbing the flow of nutrient pollution into the bay helps overall water quality, but freshwater flows are still changing the salinity of the bay and diverting some of that water could be a massive undertaking.

“Whenever these canals were put in in the late 60s it changed the drainage for our community,” Koehler said. “The tough part is: how do you take all of the water that is out in the new drainage basin and where do you put it that is not going to do harm?”

Moving water from canals poses flood risks as well as running the risk of draining private wells. 

Many who have looked at improving Naples Bay point to the Golden Gate canal as an obvious source of the bay’s impairment.

“One key to cleaning the bay is to divert the freshwater from the Golden Gate canal to a sheetflow that moves east,” Bauer said.

Collier County’s natural resources department is making an effort to tackle this very issue.

More:Four artificial oyster reefs to be constructed at Rock Creek in Naples

Called the South Belle Meade Hydration project, the idea is to divert water out of the Golden Gate canal before it reaches Naples Bay and then restore a sheetflow through Belle Meade. It’s a $30 million project, with funds coming from the RESTORE Act, which redirected a portion of BP’s civil penalties from the Deepwater Horizon spill.

The project is proposed to remove about 65 million gallons of freshwater each day from the canal, said Gary McAlpin, manager of the county’s coastal zone management team. Roughly 50% of that water will evaporate or seep into the ground, and the rest will eventually make its way to Rookery Bay.

Artificial oyster reefs protect mangroves along the shore of Naples Bay on Thursday, August 6, 2020. The artificial reefs are one of several projects being implemented to restore the bay's natural ecosystem.

Molloy said at Monday’s meeting that the Belle Meade project would remove roughly 10% of freshwater inflows from the bay.

“We’re in the design phase for Belle Meade,” McAlpin said. “We hope to be out of permitting and design in another two years and have all the permits done in another two years (after that). This is a long-term play, about a five- to seven-year project.”

Koehler said the basin is working on studies to see how effective putting water into Belle Meade is. She said flood protection and dry wells need to be considered.

“It’s another opportunity for us to take water out of the system and back onto the land,” she said. The study kicked off last month and should be done by Christmas 2021.”

The city manager in Naples, Charles Chapman, said the Belle Meade project is on par with reservoir projects in the Comprehensive Everglades Restoration Plan.

“It’s massive in its design,” he said.

With a host of problems afflicting the bay and potential solutions bubbling up throughout the area, Bauer’s original 20-year plan remains a focus at what would be its 10-year anniversary.

Bauer, now living farther north in the state, looks at the efforts that went into restoring Tampa Bay and asks, “why not Naples?”

Tampa Bay, much larger and with a much denser population surrounding it, had its own set of unique problems, different from those of Naples Bay. A 30-year process that began in the 90s has restored seagrass beds to the healthy conditions only found prior to the 1950s, said Ed Sherwood, senior scientist for the Tampa Bay Estuary Program.

“There was a collaborative partnership between public and private interests to clean up nutrient discharge, industrial wastewater and stormwater discharges,” he said. “The efforts have led to tremendous water quality improvements that allowed seagrass to grow.”

More:Naples Bay project to improve water quality on track for 2018 start

And while the problems plaguing the two bays are different, a key component on both fronts has been implementing incremental projects through a collaborative process.

The sun rises over Rock Creek in Naples on Thursday, August 6, 2020. The creek is one of many fresh water sources that feed into Naples Bay.

“It’s a great program in Tampa, but it really is apples-to-oranges,” Molloy said. “Naples Bay really is at the mercy of a much larger watershed. We’re trying to work with the county on measures that can be taken upstream to help improve water quality and decrease freshwater quantity.”

It’s the smaller efforts combined that make the bigger difference, she said. Individual projects add up to better water quality for the bay: rain gardens and filter marshes, diverting freshwater from the bay and the proposed mangrove project. These are all the efforts that can be done collectively to have a combined effect on water quality.

“Eat the elephant one bit at a time,” she said.

Karl Schneider is an environment reporter. Follow him on Facebook and Twitter: @karlstartswithk, email him at