Clean drinking water is still not widely available around the globe and therefore remains an unsolved issue. In fact, 1 in 9 people lack daily access to safe water and sanitation. Groundwater is a water supply source that needs minor treatment and thereby presents itself as a good solution to this global issue. Especially in development countries for example in East Africa this would be a viable solution. One interesting exploration method to detect groundwater in an area is airborne Frequency Domain Electromagnetic (FDEM) survey. However, most airborne EM survey instruments are expensive and bulky. Even though that this exploration technique has been around since the 50s, a commercial inexpensive airborne FDEM instrument has still not penetrated the market. This thesis describes the investigation of a novel portable FDEM survey instrument that will be employed by an Unmanned Aerial Vehicle (UAV). The system architecture for the measurement instrument is presented and the functionality, design considerations and requirements of each system block is given. To check the feasibility of the proposed architecture, a handheld Proof-of-Concept is implemented, which can carry out measurements between 100 - 12.000 Hz. The experimental measurement results of the Proof-of-Concept at operating frequencies of 925, 2175, 5025 Hz are presented and compared against measurements of GEM-2A instrument, which is employed as a reference.