The main action that the Judicial Branch can use to check the actions of executive agencies is through a process known as judicial review. If a suit is brought before the courts, a justice or justices can review the actions taken by a governmental agency involved. If they determine that a violation of the Constitution has occurred, the courts can order the Executive Branch to rectify the issue. While the courts have this power, it is seldom used. For one thing, the Judicial Branch usually tries to remain non-partisan. Overturning the actions of the Executive Branch can potentially tarnish this image. Furthermore, the courts tend to defer to the agency's expertise as long as the action is consistent with the intent set by the legislature. Interestingly, this important check on the Executive Branch is not enumerated in the Constitution. This power was established by the court itself with the case of Marbury v. Madison in 1803.
Furthermore, although justices are nominated by the president, they cannot be fired by him. Only Congress has the power to impeach and remove a federal judge. This gives the judicial branch the freedom to review the actions of executive agencies without fear of reprisal from the president.