Essentially... Hours and hours of research.
I tend to use existing zoos and do alternate takes on them, so usually it starts by looking at where the current zoo stands today in terms of location, history and style; and see what I could change along the timeline to get a completely different outcome. By then I usually have decided the theme of the zoo.
So first of all I start researching the history of the existing zoo. Usually that means buying/reading books, watching documentaries, watching YouTube walkthroughs, etc. Then I start by checking zoos in the same country or neighbouring countries for both inspiration for the zoo itself and for the animal lists. When I have a good idea of what kind of animals I can use, I start mapping out how the zoo would be split up and how they fit in with the theme of the zoo.
And then the pinterest board gets made and I start collecting as many references as I can. I look at specific exhibits for specific animals, I look at specific scenery pieces I want to include, I look for pictures that capture the general atmosphere.
By then I have mapped out animal lists per section of my zoo in some spreadsheets, I have an idea of what I want to build, I usually have a logo designed and I already have a map on which I build blueprints whenever I feel like it.
And after all that. After hours, days, weeks, months of research, planning, blueprint building. After all that.... I stare at the map and try to make an entrance and end up building in Tharmachati again.