According to an interview with the Electronic Intifada and reported by Rolling Stone, Waters said he believes it's "the most effective way to go because the situation is that the Israeli government runs an apartheid regime in Israel, the occupied territories and everywhere else it decides."
Waters also said he's considering creating a single urging artists to not play Israel in the same vein as the 1980s single "Sun City" which highlighted South Africa's apartheid policies. He plans on speaking with E Street Band guitarist Steven Van Zandt regarding it. And he's about to publish an open letter to "all my colleagues in the music industry, asking them to join me in the Bds (boycott, divestment and sanctions) movement."
But it's the boycott which he is currently focused on.