Abstract This work is an in-depth analysis of the performance behavior of a small scale single effect thermal desalination plant. The prototype, which refers to the distributed micro cogeneration field, consists of a 1 kWe Stirling engine coupled with a single effect thermal desalination plant for the simultaneous production of electricity and >150 L/day of fresh water. The prototype was able to work in two different operation modes: batch operation and continuous operation. In the former, the evaporator tank is initially filled with the salt water up to its maximum and the evaporation process ends as the salt water level reaches the top of the coil. In the latter, concentrate is continuously extracted and salt water is fed inside the evaporator tank in order to maintain brine salinity almost constant. In a previous work authors investigated the plant performance in batch operation mode finding a good agreement with the predicted results. In this work, plant performance is evaluated in continuous operation and compared to the batch operation mode. In both cases, fresh water production reached a maximum of about 7 L/h in the best operating conditions. However, despite the higher complexity of the plant, performance is worse in the continuous operation mode due to the negative effect of the continuous seawater flow. Indeed, the lower the salt content of the treated water, the lower the fresh water production due to process limits which will be extensively discussed in the paper. More precisely, the plant's average productivities were about 1.3 L/kWh and 1.16 L/kWh of thermal energy input in batch and continuous operation modes respectively. In any case, the apparatus exhibited a very good response to varying thermal power input thus confirming the opportunity to feed the desalination plant also with different forms of waste heat. Hence the proposed solution, studied for a coupling with a 1 kWe Stirling engine, can be easily applied also to the other micro-CHP technologies.