The National Park Service will wait until 2013 to again make plans for rebuilding Yosemite Lodge — 16 years after a flood wiped out half of the motel’s accommodations.

A plan to rebuild the lodge had been on the books for years, but officials dropped the $39 million project and many others last fall as part of a lawsuit settlement. The settlement ended more than 10 years of legal wrangling over protections for the Merced River, which runs through the heart of popular Yosemite Valley.

Yosemite officials last week filed papers in federal court in Fresno withdrawing the plans for about $100 million in projects. Officials are supposed to start from scratch on the projects after the river plan is completed in December 2012.

Officials agreed the river plan must come before the construction to protect the ecosystem from the development and crowds. Activists — Friends of Yosemite Valley and Mariposans for the Environment and Responsible Government — are delighted.

“Yosemite is giving itself the opportunity to base planning on a fundamentally environmental document, the Merced River Plan,” said Greg Adair, representing Friends of Yosemite Valley.

Other projects include the renovation of Curry Village, campground replacement and bridge construction.

Over the last decade, officials have failed to deliver a legally defensible plan to protect the river’s banks, vegetation and creatures from Yosemite crowds. Activists successfully argued construction projects should not move forward until the river is legally protected.

The park gets more than 3.5 million visitors each year, and more than half of them pass through the valley.

In 2000, Yosemite officials issued a river-protection plan that was supported by environmental titans, such as the Natural Resources Defense Council and the Wilderness Society. But the two local activist groups argued the construction could not take place without a specific visitor limit to protect the river.

All but a few of the construction projects were put on hold during the litigation.

In an attempt to answer criticisms, Yosemite officials rewrote the river plan in 2005. Officials said they would closely monitor crowds and prevent them from trampling the river’s ecosystem. But again the plan did not have a visitor limit.

In 2006, a federal judge ordered another rewrite of the plan and told Yosemite officials not to proceed with reconstruction projects. Yosemite’s appeal of the decision failed, and officials last year started from scratch again on the river plan.