Some significant issues remain up in the air as two major projects at the Port of Miami get ready to kick into high gear, both promising thousands of new jobs.

The construction of the port tunnel and the dredging project that will allow mega container ships from an enhanced Panama Canal to enter the port will change how Greater Miami does business — more employment and revenue from a deeper port; a downtown free of traffic-clogging trucks.

We have long supported the dredge and tunnel, but there remain some worrisome concerns that the fragile ecosystems of Biscayne Bay are about to take a real beating. Those must be resolved.

Despite assurances from the Army Corps of Engineers, which will be in charge of the dredging project, and port project managers, there are still some big question marks hovering — question marks that authorities need to eliminate for the good of the bay, the sea life it sustains and the economic boost it gives this community in commercial fishing and as a recreational attraction.

The dredging project will take the inner channel, west of the Atlantic to 50 feet deep from the current 42 feet of depth. Moving seaward, east of the stone jetties, the bottom will go to 52 feet from the current 44. The deepening will be achieved through months of blasting, destroying living coral and sea grass beds. Right now, the Army Corps of Engineers’ permit application has yet to be approved by the state Department of Environmental Protection. Several discrepancies between the project parameters approved by Congress and what DEP is seeking have arisen, especially with the subject of mitigation. The Corps has federal approval to replant eight acres of coral reefs. The Corps says that DEP, though, seeks 25 acres. Similarly, the size and location of sea grass to be resettled is in dispute.

A coalition of environmental organizations is considering stepping into this breach, filing an appeal to the Corps’ permit application. Though the organizations are asking many of the right questions, an appeal stands to cause an interminable delay in the project, slated to start in summer 2012 to finish by 2014.

It’s time for the stakeholders to sit down and hash this out, with saving the most coral and sea grass possible the priority.

As for the tunnel dig, debris — tons of it — will be deposited on Virginia Key, an environmentally sensitive, but long-abused, barrier island. Those tons of dig material are slated to become berms to hide a sewage treatment plat there, and to form a cap on a landfill. Then bike trails and a park are slated to be built.

But before that cap permanently bars access to the landfill, it’s critical the material already there be assessed for dangerous toxins leaching into the water. Virginia Key is a Critical Wildlife Area within the Biscayne Bay Aquatic Preserve.

These projects, clearly, are not being done on the fly. For years, agencies from all levels of government, from Congress to the Corps to the state DEP to Miami-Dade County’s Department of Environmental Resource Management have studied and tested and vetted various aspects of these massive projects.

Expectations are high. Recently, the director of the Port of Miami and the top administrator for the Panama Canal Authority signed a memorandum of understanding, solidifying an alliance to undertake joint marketing, technical and data-sharing activities.

The changed landscape continues to become a reality. But there’s only one chance to get it right.