As the decade turned, Linney's career continued to rise, as she added critical acclaim to her commercial success. She received her first Oscar nomination, for Best Actress, for her role in the 2000 film "You Can Count on Me," (per IMDb) which also marked the directing debut of filmmaker Kenneth Lonergan. In the film, Linney portrayed Sammy Prescott, a single mother trying to keep control of her life while her brother is in town.

Linney followed it up with a Emmy win for Best Actress in her first nomination, for the 2001 TV film "Wild Iris," in which she played Iris Bravard, a mother to a teenage son trying to cope with the suicide of her husband and the fraught relationship she has with her mother, played by Gena Rowlands.

Linney followed that up with a second Emmy win, this time for Outstanding Guest Actress in a Comedy series, for her role in the eleventh season of "Frasier." In the show, Linney plays Charlotte Connor, a matchmaker Frasier goes to see, whom he discovers has only five clients and effectively scammed him. Frasier develops feelings for Charlotte, which she seems to reciprocate, although she maintains a tumultuous relationship with her boyfriend. However, the two get together when she does break up with her boyfriend, only for the relationship to come to an abrupt end when Charlotte decides to move to Chicago. "Frasier" ends with Frasier on his way to Chicago in an attempt to reconcile with Charlotte and rekindle their relationship.