The Secretariats of the Basel and Stockholm conventions are administered by the United Nations Environment Programme (UNEP) and are located in Geneva, Switzerland. The Secretariat of the Rotterdam Convention is jointly served by UNEP and the Food and Agriculture Organization of the United Nations (FAO). It is based in Geneva, Switzerland, and in Rome, Italy.

In 2012, the Secretariats of the Basel and Stockholm conventions, as well as the UNEP-part of the Rotterdam Convention Secretariat, moved from three separate secretariats with a programmatic structure to a single Secretariat with a matrix structure serving the three conventions. Since October 2014, Mr. Rolph Payet is serving as the Executive Secretary of the Basel, Rotterdam and Stockholm Conventions. The FAO-part of the Rotterdam Convention Secretariat is currently headed by the Executive Secretary, Mr. Bill Murray.

The mandates of the Secretariats are laid out in Article 16 of the Basel Convention, Article 20 of the Rotterdam Convention and Article 19 of the Stockholm Convention. The principal functions are to prepare for and service meetings of the conferences of the parties and its subsidiary bodies, to receive and convey information, to assist or facilitate assistance to parties upon request and to coordinate with other international bodies.

The budget of the Secretariats and their staffing are determined by the conferences of the parties and are funded by contributions from parties, based on the United Nations scale of assessment.