the water separator, such as it is, is integral to the fuel filter. there is a small, plastic knob on the bottom of the fuel filter. it's usually white in color.
unscrewing this knob will allow whatever has settled to the bottom of the fuel filter to be drained out. i'll advise you to be very cautious with this plastic knob. it's not very rugged - and cracks easily. it seems like they get brittle over time.
i'm yet to find any water in my filters, but i certainly can't hurt to check, especially this time of year.
i hope that helps. if you need assistance locating the fuel filter, i'm afraid i can't be much help. i know the beetles pretty well, but i'm not familiar with your model. i'm sure someone else will chime in shortly and fill in the gaps i've left.
good luck!
mark