A major issue in long-term operation of micromachined Joule-Thomson coolers is the clogging of the microchannels and/or the restriction due to the deposition of water molecules present in the working fluid. In this study, we present the performance of a microcooler operated with nitrogen gas with different moisture levels. Relatively low-purity nitrogen gas (5.0) is supplied from a gas bottle and led through a filter to control the moisture level. The filter consists of a tube-in-tube counter flow heat exchanger (CFHX) and a heat exchanger that is stabilized at a certain temperature by using a Stirling cooler. The set-point temperature determines the moisture level at the exit of the heat exchanger. It is found that the moisture level has influence on the mass-flow rate during the cool down. Once the microcooler reaches the set cold-end temperature, the main deposition area shifts into the CFHX and the moisture level at the restriction is almost independent on the inlet moisture level of the microcooler. The moisture level at the restriction increases with the increasing cold-end temperature when the cold-end temperature is lower than the saturation temperature of the water in the nitrogen gas. Higher cold-end temperature results in higher clogging rate.