I was actually surprised at the symbolism Del Toro put in this film, and because it was my first viewing, it totally went over my head.
The two main colors in the film were green and red. Green was meant to represent isolation, and you see a lot of green things to go along with that (as well as items that were "sort of" green). Like Eliza's wallpaper, her uniform for work, the candy the bad guy was eating, the Amphibious Man's skin, the lighting in the room he was chained up in, the jello pie Eliza's next door neighbor kept eating, the jello in the advertisement, and the bad guy's car.
Red stood for connecting, like when Eliza wore red shoes after her first night with the fish guy, or the red coat she wore in the final scene.
If you look at the hallway between Eliza and her neighbor's apartments, you can see half of it is red, and half is green, symbolizing a balance between the two.
I'm afraid Del Toro rather hit the audience over the head with the color symbolism. Even in the first viewing, the red clothes were an obvious statement that her passions were being unleashed.
Although I don't know if he was consistent enough with the use of color... at the very end, when the lovers are together forever, they're surrounded by... a huge swath of blue-green.