The West Wing, like many serial dramas, stretches storylines over several episodes or entire seasons. In addition to these larger storylines, each episode also contains smaller arcs which usually begin and end within an episode.

Most episodes follow President Bartlet and his staff through particular legislative or political issues. Plots can range from behind-closed-doors negotiating with Congress to personal problems like post-traumatic stress disorder, from which Josh suffers during the second season. The typical episode loosely follows the President and his staff through their day, generally following several plots connected by some idea or theme. A large, fully connected set of the White House allows the producers to create shots with very few cuts and long, continuous master shots of staff members walking and talking through the hallways. These "walk and talks" became a trademark of the show. The final two seasons presented a narrative change, with the focus of the show divided between plots in the West Wing with President Bartlet and his remaining senior staffers and plots revolving around the rest of the main cast on the campaign trail for the 2006 election.

In the first season, the administration is in the middle of its second year and is still having trouble settling in and making progress on legislative issues.

The second season covers the aftermath of the shooting at Rosslyn, the 2000 midterm elections and dealings with a new Congress, and sees scandal when the White House is rocked by allegations of criminal conduct and the President must decide whether he will run for a second term.
The third and fourth seasons take an in-depth look at the campaign trail and the spectre of both foreign and domestic terrorism.

In the fifth season, the president begins to encounter more issues on the foreign front, while at home he faces off with the newly designated Speaker of the House, battles controversy over Supreme Court appointments and oversees a daring plan to save Social Security.

The sixth season chronicles the quest to replace President Bartlet in the next election, following the primary campaigns of several candidates from both parties, while the President himself attempts to build his legacy, but finds his ability to govern compromised by his illness.

In the seventh season, the president must face a leak of confidential information about a secret DoD program from inside the White House, while the Democratic and Republican candidates battle to succeed him in the general election.