I would like to put forth my very solid, 100% correct, theory about the ending of The Shape of Water.
While he’s now a big mainstream director, Guillermo Del Toro is very much a filmmaker from the “Magical Realism” tradition. When he makes magical realism films, they are ambiguous as to whether the fantastic elements even occurred at all, or was it just the wishful point of view of a character troubled by a horrible reality (Pan’s Labyrinth, Devil’s Backbone). In this case, the monster isn’t imaginary. He’s in a lab, in the real world. Everyone sees him. Elisa’s ultimate fate is the fantasy.
The two times we see Elisa living happily underwater are at the beginning (taking a nap in her underwater apartment, which clearly didn’t happen), and at the end (when she is magically resurrected from the dead and becomes a fish lady.) Neither of these instances are part of the main plot. It is being narrated, and the story is being told from the point of view of Giles - who is speculating/wishful thinking/spinning a yarn.
Bottom line: Giles did not witness what he’s describing. It’s how he likes to think about it.
PREFACE: ‘If I spoke about it - if I did - what would I tell you? I wonder. Would I tell you about the time? It happened a long time ago, it seems. In the last days of a fair prince’s reign. Or would I tell you about the place? A small city near the coast, but far from everything else. Or, I don’t know... Would I tell you about her? The princess without voice. Or perhaps I would just warn you, about the truth of these facts. And the tale of love and loss. And the monster, who tried to destroy it all.’
EPILOGUE: ‘If I told you about her, what would I say? That they lived happily ever after? I believe they did. That they were in love? That they remained in love? I’m sure that’s true. But when I think of her - of Elisa - the only thing that comes to mind is a poem, whispered by someone in love, hundreds of years ago: “Unable to perceive the shape of You, I find You all around me. Your presence fills my eyes with Your love, It humbles my heart, For You are everywhere.”’
So, here’s what really happened: At the end, Elisa is 100% dead. The scars on her neck were scars, because people are awful. The fish monster takes her corpse because he intends to eat it once it’s had a chance to rot a little. It’s a fish monster. It’s what they do. Giles knows this deep down, but people generally try to remember the departed charitably - even their deaths.
Let’s be serious. When the Creature From the Black Lagoon was taking all those pretty girls, did anyone think for a moment he was intending to marry them? “Make them his watery queens?” Hell no.
They were food.