After reading the reviews on this site, it is my understanding that many people that saw this move completely misunderstood it, both the people that loved it and the ones who hated it.
The theme of the movie is not something similar to Beauty and the Beast for those who might think that!
There are several themes in this movie, but the overall theme is about minorities and how privileged people view those who are different. However to make this message more clear the movie is set in the 1960's, where minorities were generally marginalized.
The lead character Elisa Esposito is a mute woman, who was an orphaned child that was found in a river with wounds on her neck and communicates through sign language. She works in a government laboratory as a cleaning lady. Her friends are her co-worker Zelda, a black woman who serves as an interpreter for Elisa, and her next-door neighbor Giles, a closeted gay man. Elisa discovers a mysterious creature in the facility and begins to bond with it. The creature is a mute humanoid amphibian that was captured in a river in South America by Strickland, who is in charge of the project to study it.
Elisa is the main protagonist in this story, and together with Zelda and Giles, they represent a social minority. Women, handicapped people, black people and gay people are all amongst those that were outcast by society at the time. On the other hand, there is Strickland who is the main antagonist in the story and he represents the privileged people at the time. He is a white man in a privileged position, married with children, religious, and is hostile to those who are not like him. He treats the creature hostilely, beats and abuses it, and calls it a monster.
When Elisa learns that Strickland plans to vivisect the creature, she hatches a plan with the help of her friends to free the creature and keeping it in a bathtub at her apartment and planning to set it free in the ocean. Elisa and the creature bond romantically and it is revealed that the creature has healing powers.
When the day arrives to set the creature free, Strickland arrives and shoots Elisa and the creature. The creature heals itself and kills Strickland. The creature takes Elisa and jumps into the ocean where it heals her. When the creature applies his healing touch to the scars on her neck, she starts to breathe through gills.
Here is the TWIST: This scene reveals that Elisa was of the same kind as the creature all along. She just had a more human like form than the creature. There are different clues throughout the film. She was found as child next to a river like the creature. She was found with the "scars" on her neck and they turned out to be dormant gills as the creature healed her. She was mute like the creature. She loved being in water as shown in her morning habits. She was initially attracted to the creature whereas most people would fear it. She comes from a Spanish speaking country, as her last name is Spanish whereas the creature was found in a river in South America.
The creature itself and Elisa represent a minority, as they are alike. The fact that the creature is different yet human like, symbolizes how privileged people viewed minorities at the time. The point of the monster is simply to symbolize how we sometimes view other people that are different from us.
The message of the story is this: You view other people that are different from yourself as "monsters" if you don't try to understand them. However, if you try to understand people who are different from yourself, then you will see that we are basically all alike even though we look different.
I think this movie was brilliant and very clever. Guillermo Del Toro did a great job. It is definitely a movie worth watching.
This is my point of view and I hope that you found this helpful.