How to scan a watercolor

1. Choose the grain.

Basically, a scanner is a line of violent light that sweeps along a document in one direction, while an array of capacitors reads the area. It's fairly vertical read, but the lights define dark shadows on the paper, making the grain visible. Most mechanical papers have a grain direction. When scanning, you might want to try both directions by rotating the paper on the scanner bed, and see which one works best for you.

For example, I scanned this water color both ways. 

There's a 90º rotation between the two pictures while scanning, obviously, but I rotated the first image so you can see the difference. I chose the image that had the more even grain, on the right.

2.Use the histogram.

Paper is a slightly reflective surface. A scanner is a violent light that makes paper shine ( any paper). It dulls the watercolor, it's quite frustrating.  The Levels tool tool, with it's clear histogram, is a good way to bring back the original  colors . The histogram is a curve representing statistics of luminosity in your image. It's a very precise tool and once you get the hang of it, it's really simple to use. 

I made a cheap and fast video to explain how to touch up a raw scan in Photoshop:


Please ask questions in the comments if necessary, but basically I used 2 tools:

-edit > fill with the content aware option (cmd+delete)
( and a bit of work with the patch tool)
This tool doesn't exist in all the image editing  softwares

-and image>adjustments>levels (cmd+L)
this one you'll find in most image editing software

You can't make it more simple. It's not about changing dramatically the picture, at the contrary. I usually work with the watercolor in view on my desk, and just try to match what I see. 

Here's the result :

As you can see, it's not about making obvious changes, just making it pretty!

I hope it helps,