Fujimoto

Fujimoto is slender and appears to be 40-years old, but he may have lived much longer. He claims he was once human, which implies he underwent some changes in order to become the wizard he is now. This may be a clue as to why he has strange, bird-like markings on his cheekbones and around his eyes.

He has long red hair like Granmamare and his daughters, with turquoise, almost green, eyes. He wears a very strange cerulean and white-striped suit with a magenta cravat. On his ears are golden, round earrings.

Near the end, he wears a similar white-striped suit, although this time the cerulean stripes are a salmon red, and the cravat is yellow.

Throughout the movie he wears a dark magenta coat with a gold clasp at the front. It's long sleeves have holes right where the inside of Fujimoto's elbow would be, and his arms are often through the holes.

When upon land, he uses a contraption he explains is a humidifier, to wet the ground with pure sea water as he is walking along it. This may imply he cannot go on land comfortably without it, or may have a risk of death without it. Also, when seen by humans, he is described as appearing very strange and perhaps shady, or to be avoided. This is only assumed, as he means no harm to humans although he seems to dislike them, especially with the waste they throw into the ocean.

Fujimoto is placed into the role of antagonist, but he is only ever acting in what he believes is best for Ponyo. However, he is strict to his daughter Ponyo, and it may come across as him trying to control his daughter rather than keep her safe. For Lisa he is kind of a creep, who mistakes him for spraying pesticide, which is actually the purest ocean water so he can survive on land.

In his core he is a good guy, who cares about his daughters. He is just over-pessimistic. He hates humans, because humans pollute the environment, and more specifically the sea. So he uses magic to purify the sea from the humans’ waste. For that purpose he creates potions and elixirs, which if mixed correctly he pours into a well in one of the rooms in his underwater harbour. Because of humanity's destructive behavior, he becomes over-pessimistic. His wife, Granmamare adds more optimism to his mind.

The seniors get to know him better as the story progresses. For them, Fujimoto is a nice guy with strange behaviours, and one claims that he wouldn't allow anyone to be harmed

Since he was once human, he can't breathe underwater.

He learned to use magic to live longer and to purify the sea. He has worked on his elixirs since 1907. His daughter Ponyo has more magic power than him due to her not being born human like Fujimoto was. He is, however, able to create bubbles of air, or water, as seen when he is underwater himself, and when he transported Ponyo back to his underwater harbour.

He can summon Sea Monsters. He uses the monsters mostly to scout the water, and he used them to rescue Ponyo from Sōsuke.

What? This is not weed killer! This is the purest ocean water, and it keeps me from drying out on land! „
~ Fujimoto to Lisa during his first attempt to get Ponyo back.
“ It’s not your fault. I exposed you to the magic and you’re too young to understand. I have to keep the sea in balance it’s a big responsibility. „
~ Fujimoto to Ponyo while trying to feed her.
“ You can’t be human and magic at the same time sweetheart. „
~ Fujimoto to Ponyo after stopping her attempt to become human.
“ If even one living creature got in here... „
~ Fujimoto while looking around the room with the elixir well.
“ It’s been a long time, my love. „
~ Fujimoto to Granmamare when meeting her once more after an undetermined amount of time.
“ It's good to meet you Sōsuke. We've all been waiting for you, the old ladies, your mother... „
~ Fujimoto to Sōsuke when meeting him for the first time in person.
“ Try to remember me kindly... if you will. Take care of Ponyo „
~ Fujimoto's last words when asking if Sōsuke will take care of Ponyo

His daughters have more magic power than him, which may be because their mother is a goddess, and they were not born human. In addition they are rebellious, and while Ponyo showed signs early in the movie, Ponyo's Sisters showed this nature later on in the film.
His wife leaves him alone often, because she travels on the sea around the world. Her duty as a goddess is to protect the sea, a similar job to Fujimoto's.
It is unclear as to why Fujimoto became a wizard in the first place, but a reason could very well be that when he was human he wanted to protect the sea, and could not do it as a human. However this is only speculation.
He appears to be quite smart, although he may have a short temper.
He messes with his hair whenever he gets stressed or annoyed.

Freakshow (by Lisa)
Evil Wizard (by Ponyo)

Sea wizard
Researcher
Marine biologist (possibly; formerly)

Sea-related magic
Sea purification
Air and water bubble creation
Living wave summoning

Purifying the ocean.
Making and using potions and elixirs.

Keep the ocean clean (on-and-off).
Keep Ponyo under his control and away from humanity (formerly).
Save the world and mankind from being flooded (succeeded).

Originally a human, Fujimoto serves as the Guardian of Sea Life. Being the husband of Granmamare, Fujimoto is the father of Ponyo and her sisters. He's shocked to find out that Ponyo is in the care of a young boy named Sosuke, and has to retrieve Ponyo back before it's too late. Although, he's successful the first time, Ponyo would escape again, thus it was upsetting the balance of nature. Running out of time, Fujimoto had to find a solution to bring Sosuke and Ponyo to Granmamare and restore the balance of nature

Although Fujimoto takes the role of the antagonist in the film, he's not considered a villain since his intents are only for the greater good of the world. For example, if Ponyo is on earth without her father in her care, then the force of nature becomes unbalanced and upset. Fujimoto had never any intent to attack Sosuke, but had to since had to since Ponyo was outside of his care.

Fujimoto hates humans since he's disgusted by the pollution that they have caused to the ocean. Although, his hatred seemed to lessen once he allowed Ponyo to live with Sosuke.

Although he's hard on his daughters, he loves them deeply despite his hard exterior. He also shares a deep love with his wife Granmamare, who serves as the Goddess of Mercy and the Queen of the ocean.

Once Ponyo turned human, and the balance of nature was restored, Fujimoto eventually wished Souske good luck and the best for him and his daughter