Nagi no Asukara (Nagi-Asu: A Lull in the Sea) takes place in a world where some people live on land and some people live underwater. Although no such place exists in real-life as far as I know, real-life locations in Japan that the anime may have referenced have been identified by dedicated fans
Map image via Google maps The identified Nagi-Asu locations are in Mie prefecture on the Honshu island of Japan.
Comparison images are from the blog by kai881 and company, the above location was the first one to be identified as Hasuta train station in Kumano City, Mie. The anime scene is from the promotional video.
Another location inspiration was found near the first location, although only two were found around the train station.
He was also able to identify the shipyard referenced in the anime. Photos were taken with the permission of the shipyard and obtained by the blog owner.
This is the crane that helped identify the location. Although the lines are simplified for inclusion in the anime, they are identical.
Please visit his blog for more comparison photos from the locations he found. Now there is a visitor's note at Hasuta station for Nagi-Asu fans to leave their comments left by the blog.
Source: kai881 and his funny friends