Measurement of the net percolation from the base of a cover system into the underlying waste material is a key component of a cover system monitoring program. The units of measure (ie a percentage of precipitation or rainfall) are simple to understand for all stakeholders, which increases the importance of obtaining representative net percolation values. In general, lysimeters are used to measure net percolation across the cover material-waste material interface; however, the design of lysimeters for cover system monitoring programs in the mining industry have typically not considered fundamental aspects of lysimeter design. Lysimeter design is typically thought of as being conceptually simple, when in reality the design, installation, and operation of lysimeters is often counter-intuitive, due to the complexities of flow through unsaturated soil systems. This paper puts forward a methodology for lysimeter design while also presenting the fundamental design variables that should be considered. Lysimeter design for differing climates, cover materials, and waste materials is discussed. Finally, the performance of lysimeter designs previously installed in the field at sites in Australia, Canada, and the United States are subjected to numerical modelling to determine whether net percolation is being measured properly.