Lyric discussion by musicismylife926 

Cover art for A Bower Scene lyrics by Decemberists, The

As continued from Hazards of Love I:

A bower is a lady's house...kind of like a sorority, I'm guessing. Anyway, Margaret is obviously not getting over William and is unconsolable. I do like the previous comment about the sister being a nun...but im not sure if its right. Not to mention what cistern means. I personally cistern (which means 3 different things) Cistern I believe in this context is talking about the amniotic fluid around the baby (as in the water...) And basically yeah...who's the father?...obviously william. So Margaret leaves the bower before her pregnancy becomes too noticable.

My Interpretation

I'm thinking this makes more sense:

A woman's private chamber in a medieval castle; a boudoir.

http://www.thefreedictionary.com/bower

Thus, she's sitting in her room in a castle. I agree with the your cistern assessment.