Congress controls the bureaucracy through its power of the purse and its power to pass laws.
Congress’s control over the bureaucracy is in some ways more indirect than direct. Congress can use its power of the purse (the ability to appropriate money) to control agencies by not giving them enough money to do their jobs, or it can appropriate funds in such a way that prevents an agency from doing what it wants to do. Congress can also pass laws that restrict or prohibit certain types of behavior by an agency. For example, if Congress passed a law prohibiting the Environmental Protection Agency (EPA) from regulating greenhouse gas emissions, then EPA could not regulate those emissions.
Congress also has other tools at its disposal for influencing agencies. It can appoint agency heads based on party affiliation or political servitude (a person whose views are aligned with those of another person or group). It can also use hearings, investigations and oversight (reviewing what an agency is doing) as ways to exert pressure on agencies to change their policies or even get rid of agency leaders who disagree with congressional goals.
Finally, Congress has legislative powers that allow it to pass legislation affecting agencies or parts of the bureaucracy directly:
