The question explicitly says Congress.
In the system of checks and balances in the U.S. Constitution, the Congress has pretty much four major checks against the Presidency. It can …
- … not initiate any legislation desired by the Presidency. This has a specific subset that is important in its own right:
- … control the purse strings; withhold supply, and appropriations, until the President does as requested. Yes, this is ironic.
- … override Presidential vetoes.
- … refuse consent to Presidential appointments. (Senate only)
- … impeach the President.
There are a couple of further checks that are not in the Constitution, but that are checks that Congress has in practice, derived from historic practice in the U.K. Parliamentary system. For example, it can exercise legislative oversight and summon the executive branch to testify in Congress. And yes, motions of censure exist, and have been levelled and even sometimes passed against Presidents before, but have no legal effect, given that the Constitution makes no mention of them.
You can see, not least by the existence of questions on this WWW site such as "Legal consequences of complying with a house supoena?", that some of these are also being used.