Boaters were banned from Florida Bay for two weeks in 2013, and the idea of dredging got dredged up again.
The war against lionfish escalated the past year but biologists fear it may be impossible to ever completely rid Florida Keys waters of the dreaded invasive.
After the economic downturn slowed Everglades restoration progress, the pace improved somewhat in 2013 with about $70 million in pledges from the state.
The first new bridge over the Tamiami Trail, a one-mile span built to let more fresh water flow toward Florida Bay, opened in March with U.S. Secretary of the Interior Michael Salazar on hand. The federal government also endorsed the addition of more than five miles of additional bridging.
Among other issues affecting the Keys environment in 2013, among the least popular was the federal government's shutdown caused, by a budget deadlock, from Oct. 1 to Oct. 17. That resulted in boaters being banned from much of Florida Bay inside Everglades National Park and from Dry Tortugas and Biscayne national parks.
About 150 Upper Keys sport fishermen and guides staged an Oct. 9 protest at the Everglades park border north of Plantation Key, an event that made national news.
During the closure, park rangers politely but firmly directed errant boaters to exit at the nearest park boundary. Still, crew aboard a commercial fishing boat was arrested in the Dry Tortugas, reportedly admitting they did not expect to be caught because of the shutdown.
The Florida Keys National Marine Sanctuary closed its Keys offices for the shutdown but sanctuary waters remained open while state marine officers enforced regulations.
Duck Key dredge
A controversy over dredging on the sea floor -- an issue virtually unheard in recent decades -- reached the Monroe County Commission last spring.
The proposed project, restoring an old 700-foot-long channel leading into privately owned Walker's Island near Duck Key, was extensively planned and limited to privately owned bottom.
A real-estate group and marine contractors endorsed it. So did the county Planning Commission, which cited the plan and mitigation pledges as a reasonable compromise by Little Conch Key Development Corp. to allow restoration of a channel dug about 50 years ago.
But the precedent of digging through a shallow seagrass flat alarmed conservation and sportfishing groups who rallied to oppose it. What was left of the original channel was less than a foot deep in spots, and protected seagrass would be destroyed.
When the proposal for a plan to change the county's land-use plan allowing the dredging reached the County Commission in April, it ran hard aground and failed on a unanimous vote.
"This is plowing up the ocean bottom," County Commissioner Sylvia Murphy said. Commissioner Danny Kolhage agreed, "Approval of this [would] send a message that we're reversing what we've been doing for the last 30 years."
Even if the county had approved the channel dredging, it could have been blocked at the state or federal level.
Another debate first heard nearly 20 years ago surfaced when the Florida Keys National Marine Sanctuary started looking at changes to its network of marine protected areas as part of its management plan update.
Working groups of the local Sanctuary Advisory Council worked to create recommendations for several plan elements, with little opposition.
But when volunteers began to map suggested changes for Sanctuary Preservation Areas and Ecological Reserves that have been in place since 1997, commercial fishermen and recreational sportfishing groups began packing meetings last summer to heatedly protest the possibility of no-take zones.
The Advisory Council's schedule was moved back to allow for more meetings, then the federal government shutdown stalled things more.
Now the Advisory Council expects to make its specific suggestions -- which still must be reviewed by state and federal staff -- next spring, about six months later than planned.
The success of coral nurseries, an effort launched by Ken Nedimyer's Coral Restoration Foundation and expanded by groups including Mote Marine Laboratory, drew worldwide attention and increasing numbers of eco-tourism dive groups.
At designated underwater spots, new corals are carefully propagated and grown for eventual transplant to repair to damaged areas of the coral reef.
Those propagation sites were formally declared "zoological parks" by the County Commission in July in hopes of securing funding from sources like the BP Deepwater Horizon settlements.
War on lionfish
Lionfish, the showy Pacific reef fish armed with venomous spines that deter predators, were declared a "take all you want" species this year by state fishery managers.
The Florida Fish and Wildlife Conservation Commission in 2013 acted to allow divers to harvest lionfish without having a saltwater fishing license, which covers virtually all other fish species.
Divers who complete an education course can qualify to net lionfish inside some preservation areas, and professional dive crews are allowed to spear them. Hook-and-line anglers must have a regular fishing license but can take lionfish without limit.
Biologists fear the fast-breeding and voracious lionfish could deplete Florida reefs of native fish, as has happened in areas of the Caribbean.
Divers have reduced the lionfish population at many popular Keys reefs, but the lionfish can find a home in deep water or at smaller patch reefs.
The undersea research platform Aquarius, in danger of closing permanently in 2012, staged its first mission in September under the new management of Florida International University.
The Aquarius housed a team of astronaut trainees who practiced long periods of working in a weightless environment.
A planned 31-day mission planned by Fabian Cousteau, grandson of the famed underwater explorer Jacques Cousteau, was delayed until 2014.