There is a lot of water in this novel, and while water can do a whole lot of symbolic work, it is especially important to note that water is often tied to women's sexuality in literature. And there's a flood of female literary characters who drown (pun most definitely intended). Think of Hamlet's Ophelia or Edna Pontellier in The Awakening, for instance.
So when we see the theme of drowning arise in A Northern Light, we're not really surprised. On one hand, drowning is related to sexuality. Consider this scene when Grace visits Mattie as either a dream or a ghostly visitor:
I hear something strange then. Water. I hear the sound of water dripping.
I open my eyes. Grace Brown is standing by my bed. She's holding my dictionary in her hands. Her eyes are as black and bottomless as the lake.
"Tell me, Mattie," she says. "Why does gravid sound like grave?" (42.6-9)
Grace's ghost reminds Mattie that being pregnant, which requires some hanky-panky to happen, is kind of related to death. Not physical death, but the death of a part of oneself, though physical death is certainly a risk of childbirth. In this way, female sexuality is entwined with death, and all the more so since, at the time the book is set, women don't have the same capacity to refuse men and their advances that ladies sometimes have today.
And Mattie agrees with Grace, especially when she considers all that Minnie has given up to be with her husband. She tells us:
A year ago she was a girl, like me, and we were in my mamma's kitchen giggling and fooling and throwing apple peels over our shoulders to see if they'd make the initial of our true loves. I couldn't even see that girl anymore. She was gone. And I knew in my bones that Emily Dickinson wouldn't have written even one poem if she'd had two howling babies, a husband bent on jamming another one into her, a house to run, a garden to tend, three cows to milk, twenty chickens to feed, and four hired hands to cook for. (33.gravid.46-47)
Pregnancy, and by extension, sexuality, is the death of girlish innocence, and also the death of possibility. Minnie used to have multiple paths available to her for her future, just like Mattie has, but Minnie chose the path of traditional womanhood. For her part, Mattie isn't sure that this path won't kill her spirit.
Plus there's also Grace's death, which is literally a death by drowning. Once again, this death is related to sexuality: Grace is pregnant with Chester's child, so he kills her. If sexuality and passion are flames, then on both literal and metaphoric levels, we see women doused out throughout this book.