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I've always being a big fan of color coding different sections of the website. I think it's a great idea that increases usability dramatically. But you need to finish this. If you color coded sections of the website you need to color code navigation items respectively. I highlighted them below.
I would re-organize navigation items in following way:
- Home
- Places of interest
- Footpaths
- Safety information
- Travel information
- Library
- Gallery
- Blog
I would also remove Links item completely. If you need to provide partners links pt them in the footer.
http://www.toya-usu-geopark.org/en/footpath
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1
Green
Because Footpaths section has a green background
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2
Dark gray
Safety Information section has dark gray background
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3
Orange
Travel Information section has orange background
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4
Remove this item
Put links in the nice footer
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5
Blue
For Blog section
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6
Different color not green
Just choose another background for this section and don't forget color code this navigation item respectively
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7
Weired space
I have never seen centering in navigation items before. These spaces on the sides look very weired. I recommend aligning them on the left and definitely give some space between them to "breath"

Interesting idea to have the navigation colored as well.. Quite contrary to the reviews above which recommend more of a unified look and desing
Thanks for your review!