A system for microwave assisted high-throughput chemical processes is disclosed. The system includes a source of microwave radiation, a microwave cavity in communication with the source, and a microtiter plate in the cavity. The microtiter plate is formed of a microwave transparent material and includes a plurality of sample wells. A fluid chamber is defined by the interior of the four walls, the base, the profiles of the wells, and by the top surface of the microtiter plate. A microwave-moderating fluid in the chamber helps produce a more uniform microwave field among the individual wells in the microtiter plate when microwaves are applied in the cavity from the source.