The lawsuit was filed in Maryland federal court by the Wikimedia Foundation, Amnesty International USA, Human Rights Watch and other organizations.
It said the effort by the National Security Agency and other intelligence services "exceeds the scope of the authority that Congress provided" and violates US constitutional guarantees.
"We're filing suit today on behalf of our readers and editors everywhere," said Jimmy Wales, founder of Wikipedia, in a statement.
"Surveillance erodes the original promise of the Internet: an open space for collaboration and experimentation, and a place free from fear."
The lawsuit claims that by tapping into the Internet backbone, "the NSA is seizing Americans' communications en masse while they are in transit, and it is searching the contents of substantially all international text-based communications," effectively sweeping up data of many people unrelated to the effort to thwart terrorism.
"Rather than limit itself to monitoring Americans' communications with the foreign targets, the NSA is spying on everyone, trying to find out who might be talking or reading about those targets," said Patrick Toomey of the American Civil Liberties Union, which is representing the organizations.
"As a result, countless innocent people will be caught up in the NSA's massive net."
The lawsuit argues that based on documents leaked by former NSA contractor Edward Snowden, the NSA intercepts virtually all Internet communications flowing across the network of high-capacity cables, switches, and routers that make up the Internet backbone.
Also joining the suit are The National Association of Criminal Defense Lawyers, Pen American Center, Global Fund for Women, The Nation Magazine, The Rutherford Institute, and Washington Office on Latin America.
The defendants include the NSA and chief Michael Rogers, the office of the Director of National Intelligence and its chief James Clapper, and US Attorney General Eric Holder.
Asked about the suit, a Department of Justice spokeswoman said only that the agency "is reviewing the complaint."
A similar lawsuit was filed last year by the Electronic Frontier Foundation.