"'Goodbye Blue Sky' is all about and how I feel about the fields of the earth being bathed in blood because we're so determined to bombard our fellow man with our bit of ideology, or our bit of this, or our religion, and some took issue with that," Waters says.
Waters communicated with Anti-Defamation League national director Abraham Foxman and the rocker agreed to move the Stars of David further away from the dollar signs.
"His shows deliver messages, breaking down wall, etc. He uses symbolism, and that's one issue," Foxman told The Associated Press last week. "It's artistic exuberance and crossing the lines of whatever, but he's not an anti-Semite."
But Waters this summer opened a new chapter in the controversy when he included the Star of David, among other symbols, on one of his trademark inflatable pigs. Jewish dietary law strictly forbids eating pork.
Waters says a new set of pigs were built for the South America leg of the tour and the Star of David was one of the symbols added to them. "Since then, because of the complaints from some of the Jewish community, we've added a crucifix and star-crescent," Waters says.
But what has proved the greater concern for Foxman is Waters' support of the Boycott, Divestment and Sanctions movement, which calls for economic, political and cultural pressure on Israel to protest its policies against the Palestinians.
"Artistic license doesn't cover everything, it covers the symbolism," Foxman says, adding: "You can criticize Israel, but you cannot criticize its existence."
For the past seven years, Waters has supported the global BDS movement over concerns about how Palestinians are treated. Waters has called on Israel to tear down its West Bank separation barrier, and has encouraged other artists to follow his lead and refuse to perform in the Jewish state.
Waters doesn't see the boycott movement as a threat to Israel and points out that it has some backing in Israel itself. But most Israelis view the movement as hostile and counterproductive to peace efforts. Some even liken it to delegitimizing the Jewish state altogether.
"The BDS movement is out there to undermine Israel, not to undermine Israeli policy toward the Palestinians," says Paul Hirschson, a spokesman for Israel's Foreign Ministry.
The controversies underlie the continued power of Waters' music. When he conceived the rock opera in the late 1970s with his band, Pink Floyd, Waters wanted to capture the cause and allusions of personal alienation, hence the metaphorical wall.
For the 30th anniversary, he has taken the theme of isolation and applied a global perspective to it. He says he "feel as though I'm hurling myself against a wall metaphorically."
In addition to the Israel-Palestinian crisis, Waters has used visuals that touch on a wide range of topics during his show, including showing victims of conflict, U.S. troops killed in Iraq and the death if Iranian political protester Neda Agha-Soltan.
In its three-year span, "The Wall" show went on to become the highest grossing tour of all time by a solo artist. Waters next stop is the Broadway musical version, which begins workshops in January.