Much of the subway system was up and running within days after Hurricane Sandy. But the effects of the storm are still being felt, five years later. NY1 Transit Reporter Jose Martinez filed the following report.

From sidewalk grates to station entrances, thousands of openings allowed water to pour into the subway during Hurricane Sandy's storm surge. The MTA had only plywood and sandbags protecting against the floodwaters, but nothing more.

"We've learned our lesson — won't happen again," MTA Chairman Joe Lhota said.

In the five years since Sandy, the MTA has spent more than $5 billion repairing the damage and preparing for the next big one.

For example, the transit agency has built walls to protect the A line between Broad Channel and the Rockaways.

Floodwater protections have been installed at 48 station entrances, and are being built at 58 others. That includes vault-like doors, which are now at Whitehall Street and South Ferry, which was flooded by 15 million gallons of saltwater, and only fully reopened in June.

The MTA also has purchased so-called flood logs, which can be stacked at entrances in just hours to keep the stations dry.

"We're always going to have a 24-hour period of time in the event that we know there's a hurricane coming," Lhota said. "There's more than ample time."

As for those sidewalk grates, 2,300 coverings are now in place south of 14th Street in Manhattan.

"We're addressing the low point because water sinks to the lowest point, which is downtown," said MTA NYC Transit Program Manager Robert Laga.

The MTA has also 25 manually-cranked station entrance covers ready go in Lower Manhattan. They're made from the same material as astronaut suits and can be quickly put into place.

"We have a bunch more to install," Laga said. "The reason why we chose this product and developed this product was because of its quick deployments."

But for all the work that's been completed at subway stations in Lower Manhattan, there's still plenty ahead in other parts of the subway system, namely in the nine subway tunnels that were flooded during Sandy. Repairs are completed in four but have yet to begin in those carrying F and L trains between Brooklyn and Manhattan.

"There will be other upgrades that have to happen as well over the next few years," said Richard Barone, the vice president of the Regional Plan Association. "But it's going to go on for several more years."

Following a wakeup call from a storm whose effects are still being felt by riders.

"There wasn't really a lot of thinking about events of this magnitude before," Barone said. "There's been a lot more since, which is a good thing."