How is Walpurgisnacht's appearance predicted?
As a matter of fact, Kyoko asked Homura the same question regarding Walpurgisnacht's appearance, to which Homura responds with a single word:


  Statistics.


Well... I think you can take Akemi Homura's word for it. She has experienced so many timelines, planning and fighting the Walpurgisnacht witch, gradually learning more and more about it every time.

I suppose she's done a lot of data analytics about the witch with all the information she has collected throughout the timelines! Graphs, annotated sketches of the Walpurgisnacht witch and maps of Mitakihara city feature at Homura's residence. Also note that among the timelines shown, all of them place the fight scene of magical girls vs the Walpurgisnacht witch in one of the lakes/water bodies of Mitakihara city. 

Here's Homura indicating the location of the witch...



Edit:

I would suggest that Mami knew about Walpurgis in the first timeline of episode 10 only because Kyubey said so. After all, the Incubators do plant grief seeds across the city, which hatch into witches. In fact, I wouldn't be surprised if the Walpurgisnacht was the work of the Incubators. In all their advanced technology and magic, the Incubators may even fabricate grief seeds which has the essence of an agglomerate of regular witches...