The complete project could cost as much as $25 million and would require significant political support.
"This is one of the most spectacular small boat harbors in the world," said Harbor Commissioner Brad Avery, "and it's incumbent upon leaders to keep it that way."
The City Council will be asked in November to fund between $2.5 million and $3 million to pay for a portion of the first phase of dredging, said Harbor Resources Manager Chris Miller. The federal government has an additional $2.2 million earmarked, and Miller says the city is looking for other funding sources.
This first phase would dredge shallow areas between Balboa Island and the Balboa Peninsula, a patch south of Harbor Island, the main anchorage, stretches north and south of Lido Isle, and a small area by the Coast Guard station.
Avery, who directs Orange Coast College's School of Sailing and Seamanship, says he has been stuck many times when sailing around the harbor.
"There are worse situations to be in," he said.
Large racing sailboats are especially vulnerable, as some can protrude 13 feet below the surface.
If the City Council approves the agreement Tuesday, it would allow 45,000 cubic yards of mercury-laden material to be sent to Long Beach, where port officials are filling in old slips and building new wharfs, among other terminal improvements.
This phase would also bring roughly 300,000 additional cubic yards about five miles offshore to an area reserved for relatively clean sediment.
Miller hopes to begin work before the end of the year — soon after the Rhine Channel project is expected to be completed.
Last year, city officials finished a four-year dredging project in the Upper Newport Bay that cost $47 million.
mike.reicher@latimes.com
Twitter: @mreicher