Why would water get into the system?
I assume that you are sampling the air outside some building.
Run a pipe from your air sampler to the outside, fix the small end of a funnel to the end of the pipe, fix the funnel so the large open end is downwards.
The rain will drip off the funnel, and the air can get in.
I saw something like this at the meterological observatory at Lerwick in the Shetland Islands, where the rain comes past horizontally most of the time.
JimB