They are known as the 'panda of the sea' because of their distinctive markings.
WWF says the "number one reason" for the fall in numbers is the use of gillnets.
The devices, which are hung vertically, significantly increase the average catch size.
Many "ecologically important species" have suffered a "significant decline" because of the use of gillnets, WWF says.
Another cause is the illegal trafficking of part of the totoaba fish.
Its swim bladder is prized in China, where it is thought to ease discomfort during pregnancy and help with joint pain.
WWF claims the Mexican government has failed to enforce its own two-year ban on the use of gillnets, resulting in "unabated gillnet use".
With the ban due to expire at the end of May, WWF is calling on the Mexican government to "implement and enforce a permanent ban on all gillnets".
It also wants the authorities to "remove all ghost nets to prevent any bycatch of vaquita".
In addition, it is suggesting that the American and Chinese governments work with Mexico to stop the "illegal transport and sale of totoaba products".
An illicit trade route runs from Mexico, through the US and then on to China.
Chris Gee, from WWF-UK, said the public's help was required to "motivate the Mexican government to act to protect the species".
He added: "The last hope for the species is the Mexican government immediately putting in place and properly enforcing a permanent ban on gillnets."
More than a third of the world's marine mammal species are found in the Gulf of California World Heritage site.
It is home to five of the world's seven turtles and almost 900 fish species.
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