The money has already been appropriated but not spent and is targeted for various stateside military facilities. It's unclear which projects would be affected.

The Pentagon has identified $12.8 billion in military construction spending that could be used to fund the building of a wall on the southern border.

Washington Examiner:

Some states that have been allocated big chunks of money that haven't been spent could see a hit. California, for example, was identified as having more than $700 million in unused Army and Navy military construction that could be used. Hawaii has more than $400 million that could be used. More than $200 million in similar funding allocated for Hawaii, Maine, New York, North Carolina, Guam, Germany, Guam [sic], and Guantanamo Bay Cuba are also on the list. Reed warned in his tweet that "military bases in your state could be negatively impacted" by Trump's border emergency.

Trump Admin finally releases its list of at-risk #milcon projects that could be put on the chopping block in order to divert billions to pay for Trump’s ineffective #borderwall. Take a look - military bases in your state could be negatively impacted.

https://t.co/xJyDzjSITS — Senator Jack Reed (@SenJackReed) March 18, 2019

Reed's framing the issue as a local economic issue is clever, but hardly relevant. It's a question of priorities. Should building a new PX at a Georgia military base be given a higher priority than building a wall? That's the Pentagon's reasoning, and, given the president's declaration of a national emergency, it's not a hard call.

Not all the projects will be scrapped. Some may be delayed; other long-term projects could see reduced funding on a year-to-year basis. The allocation of money is somewhat at the discretion of the secretary.

The point is, the money is there whenever Trump wants to use it. There will no doubt be temporary court injunctions to prevent any construction immediately, but with the emergency declaration, the delay is not likely to be a long one.