As you would imagine, Japanese fans have been busy identifying, touring and photographing the real places used as backdrops for this new Kyoto Animation anime.
The show is not set in one particular place, but its backgrounds are based on locations in and around the city of Otsu 大津, at the south end of Lake Biwa, just northeast of Kyoto.
Here is one fan's Google Map, which I hope will continue to be filled in. Here are one blog's pages for the OP and ep1, and for eps 2-3. I hope that blogger will continue as the episodes progress. And here is another blog's compendium of scenes.
For example, here is a montage of the scenes at the end of the OP, along with a photo of a real place, the double railway bridge over the Setagawa River 瀬田川 at Ishiyama 石山, in the eastern part of Otsu:
Now here is a scene from episode one, with its real-life location on the platform at Anou Station 京阪穴太駅, northwest of Otsu:
The school scenes use the Old Kaigake Elementary School 旧鎌掛小学校 at Hino 日野町, in the countryside southeast of Otsu:
From the overview of the school, you can see how the artists just use photos as a basis, but make whatever changes they want:
Here's a scene from the OP, with its location at Karahashi Park 唐橋公園, next to the Setogawa road bridge at Ishiyama:
And here is another scene from Karahashi Park:
Even surrounding residential streets get into the action. Here is a street east of the railway crossing north of Anou Station:
Finally, here is a video posted October 8 of one fan's visit to the area:
For no particular reason except my love of The Tale of Genji, I have to add that Lady Murasaki is supposed to have started writing that novel in August 1004 AD, when she was living at the Ishiyama-dera temple, on the river about a mile south of the big bridges shown in the anime.