The agency, which was founded in 2002, specialises in working with brands and businesses to understand how sustainability can improve business performance.
It offers clients a number of proprietary tools, including Steer, a self-assessment tool that helps identify the risks and opportunities for brands engaging in the sustainability agenda. Clownfish will slot into Isobar, Aegis' digital agency network.
Clownfish and Aegis Media already work in close partnership for clients including Coca- Cola, Reebok and Beiersdorf. It will open a new office in Shanghai in November.
Robert Lerwill, the chief executive of Aegis, said: "Clownfish is a highly strategic investment for Aegis in a high potential space. We know the Clownfish team well, and respect both their approach and the results they get.
"This acquisition will better help our clients, by linking marketing communications and sustainability in a robust and meaningful way. It is also a key plank in our own sustainability strategy, demonstrating our corporate commitment to an important area."
Diana Verde Nieto, the chief executive of Clownfish, added: "Of all the people we have worked with and talked to, Aegis has shown its commitment to sustainability.
"With that commitment, the unique capability in Isobar and our own expertise, I believe we can make a real difference."