The basic trick to maintaining water separators in cold weather is draining them daily. Obviously, the time to drain is just before shutting down while the fuel and any separated water are still warm. Once the water in the bottom of the bowl freezes, it has to thaw out during operation for you to drain it. If there’s a lot of water in the fuel, you could end up unable to drain until the water level in the bowl is too high to allow effective separation.
The plastic bowl is sometimes a bit opaque, making it hard to see for sure whether or not there is any water in it. Regular draining helps you be sure the fuel in the bowl is dry. Open the petcock and drain the unit into a safe container. You’ll smell diesel fuel as soon as it emerges.
There are two types of units: self-venting and non-self-venting. The problem is, if you are going to remove fuel, you must replace it with something or create a vacuum in the system. Self-venting units immediately sense a drop in pressure below outside air pressure and open a valve to allow some air into the system during draining. With non-self-venting units, Ken Stirn of Baldwin says you need to just turn the filter to loosen it and break the seal so air can get in and replace the drained fuel.
Fuel filtration systems usually include a priming pump. Retighten the filter if you’ve loosened it, then operate the pump to refill the unit with fuel after draining. If there’s no pump, you may have to crank the engine to refill the system with fuel. The best procedure is to install (or spec on new equipment) a filter unit with a priming pump.
Some separators come with an indicator light that illuminates when electrical sensors detect water in the bowl. These systems save you the time and effort of daily draining, especially when you are using high-quality fuel.