Total costs for the $4.65 billion 520 floating-bridge project have been revised downward, but a new problem has arisen: cracks in a couple of the new pontoons.

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Good construction progress and a pending federal loan of $300 million have reduced the funding shortage on the Highway 520 floating bridge to $1.4 billion, state Transportation Secretary Paula Hammond announced.

An agreement for the federal loan was signed Thursday, she said.

At the same time, though, there are new problems to contend with — cracks appeared in two pontoons that arrived in Lake Washington this summer from Grays Harbor, where they were built. One of them is still leaky after the first attempt at sealing failed, Hammond said, so experts are looking at other methods.

“It’s apparently not holding up in the repairs that have been done to date,” she said. “I personally think it’s doable.” Hammond said the state won’t accept the pontoons from the contractor, Kiewit-General-Manson, until they are watertight.

In particular, DOT is concerned about “Pontoon W,” the big endpiece that goes on the east side of the floating bridge, where it will be exposed on three sides to weather and lake water.

Some of the cracks are superficial and some are structural, said Mike Cotten, a design-build manager for the state Department of Transportation. Water hasn’t been streaming in, but some of the cracks have allowed absorption and condensation so water appears inside the pontoon, Cotten said.

Still, the larger financial picture has improved, Hammond said.

The project was estimated to cost $4.65 billion, but lower than expected bids and ongoing construction progress for the bridge’s east approach and floating sections have resulted in experts at DOT revising the overall costs downward, to $4.13 billion.

Taking those savings, other adjustments and the federal loan into account, the DOT says its former $2.1 billion funding gap for the project is now roughly $1.4 billion.

This improves the odds that if lawmakers put a toll on Interstate 90, it would raise enough money to complete the largely unfunded Seattle section of the project.

The Seattle section remains controversial, and some neighborhood advocates want only a four-lane crossing — not the wider six-lane version that DOT has planned.

The federal loan is meant for a so-called “Lake to Land” segment, in which Hammond proposes to build the westbound lanes from the bridge’s west high rise to the Montlake interchange.

“With this funding, we will continue to make progress on replacing the most vulnerable structures in this SR 520 corridor,” she said.

The Coalition for a Sustainable 520, a collection of neighborhood advocacy groups, objects that traffic would be deposited at Montlake before DOT can fund long-promised parklike lids.

Another unsolved problem is what type of fixed bridge to build over Portage Bay near Interstate 5, and whether the bulk of that structure would overwhelm its surroundings.

Mike Lindblom: 206-515-5631 or On Twitter @mikelindblom.