Watson was elected to Congress in a 2001 special election to fill the vacancy caused by the death of Representative Julian C. Dixon. She was re-elected four times, and retired after the end of the 111th Congress.
Watson was elected to the California State Senate from 1978 to 1998. The longtime chair of the Health and Human Services Committee, she gained a reputation as an advocate for health care for the poor and children. She was the first African American woman in the California State Senate.[7] Term limited, she was replaced by Kevin Murray.
When, in 1988, the US government proposed the addition of the category of "bi-racial" or "multiracial" to official documents and statistics, some African American organizations and African American leaders such as Watson and Representative Augustus Hawkins were particularly vocal in their rejection of and opposition to the category. They feared massive defection from the African American self-designation.[citation needed]
In 1999, President Bill Clinton appointed her United States Ambassador to Micronesia and she served in the post for two years. She stepped down to run in the April 2001 Democratic primary election, which was called to nominate a candidate to replace Congressman Julian Dixon, who had died in office five months earlier. She won with 33 percent of the vote in a multi-candidate field, then carried the district with 75 percent of the vote in the June 2001 special election.[8]
In Congress, she became a vocal leader on issues related to racism and xenophobia, supporting reparations for descendants of American slaves, reform of the educational system, subsidies for families lacking health care, and a comprehensive overhaul of the nation’s criminal justice system. She also decried incidents of violence and racism against Arab Americans that she believed were a result of retribution for the September 11, 2001, terrorist attacks.[9]
On the issue of Cherokee Freedmen citizenship in the Cherokee Nation, Watson noted that 20,000 Cherokee lived in California. She opposed the Cherokee Nation's March 2007 vote to amend its constitution to limit citizenship to only those descendants with at least one Indian ancestor on the Dawes Roll. She noted that when freedmen were granted citizenship in the tribe in 1866 by a treaty which the Cherokee Nation made with the US government, it was without restriction to those freedmen with Indian ancestry. Appeals to the Cherokee Nation's position were pending, in part because the tribe excluded descendants of Cherokee freedmen and intermarried whites from voting on the amendment. In June 2007 Watson introduced a bill to sever US relations with the tribe and revoke its gaming privileges unless the Cherokee Nation restored citizenship in the tribe to descendants of Cherokee freedmen.[16] This drew the ire of several tribal leaders and individuals in Indian Country, accusing her of undermining Native American tribal sovereignty.[17]
Throughout her career in Congress, she advocated for increased funding and research directed at the HIV/AIDS pandemic. She argued in favor of humanitarian assistance for African nations that had been decimated by the disease.[19]