I followed a tutorial on GTK which used this command to generate the build flags:
$ pkg-config --cflags --libs gtk+-3.0
This outputs coherent flags. From research, I have found that pkg-config searches for .pc files in /usr/lib/pkginfo, usr/share/pkgconfig, in the /local equivalents, and in the folder indicated by the PKG_CONFIG_PATH variable.
None of the folders contains the GTK file and the environment variable is not set. Where is pkg-config getting the flags?