This link may be relevant to your situation. I came across it while doing some research on water level / moisture sensors for my hydroponics system. The link itself is information on a pcb which is being used as a basic planar capacitor to measure soil moisture levels. But, it sounds like you're using something similar.
I think with NETMF being an interpreted language, you're going to have issues with measuring the timing.
If you scroll down to the comments at the bottom of the page, you'll find links to some basic specialized circuits which will allow you to translate the PWM signal into a constant analog voltage that you can measure from a Netduino. It takes a lot of the timing issues out. Hope this helps.