You can see which secret flowers you are missing by looking at the pots: There's three green leaves on each of them that indicate if you have found the secret flowers in a level!

Secret Flower 1:
Instead of progressing to the yellow flowers first open the light purple ones that are scattered in a big circle around the valley.
As soon as you opened enough of them the secret flower spawns.

Secret Flower 2:
It's basically the same as the first one. Open the light purple "optional" flowers that are around the outside of the area.

Secret Flower 3:
Behind a rock behind the big tree at the end of the level.

Secret Flower 1:
After you've bloomed all the flowers in the first section and the valley turned green they appear on the left on top of a hill close to the gate. Don't forget to activate the stone circles and the little Flower "paths" they make.



















Secret Flower 2:
Bloom all the flowers and turn the grass of the valley green and blue. As soon as you bloomed everything the flowers will appear.

Secret Flower 3:
When you go into the last field turn left, the flowers are in a small nook on the side of it.

Secret Flower 1:
Once you bloom all the flowers in the first area with the windmills this one will appear in the middle under the big windmill. If you already activated the canyon but the secret flower didn't appear yet you missed a flower to bloom.



















Secret Flower 2:
While you are going through the canyon, try to stay up and to the left until you get to this part:
Keep left and go into the cave, you'll find the secret flower there. Additionally, if you keep right in the second cave you'll get the "Flow" Achievement.

Secret Flower 3:
As soon as you get out of the canyon turn back, stay on the ground and to the right and go back in. The flowers are in front of a stone.

Secret Flower 1:
When you reach the haystacks go straight past them. The sceret flowers are behind a roll of hay.



















Secret Flower 2:
After activating the "light spiral" go through the cart that lies next to the lantern and fly through it.



















Secret Flower 3:
Before finishing the last patch of light go to the little pond that is behind the spiral and the wheelbarrow where the previous flower was and light it up. You'll also get the "Illumination" Achievement for it.

Secret Flower 1:
Directly at the start fly up and to the left. The secret flowers are in a small valley.



















Secret Flower 2:
In the area where you have to deactivate the three big power lines bloom all the flowers but keep the light purple ones under the tower for last. After you bloomed these, the tower will topple over and the secret flowers will spawn underneath.



















Secret Flower 3:
When you go into the maze stay up and stick to the right wall until you get to this point:
The flowers are on the right.

Secret Flower 1:
The flowers are on a steel beam inside the right skyscraper in the second are of the level.
To get there use the fan on the left next to the entrance and follow the path of flowers over the roof, then enter the skyscraper from the top.

Secret Flower 2:
When you get to the highway exit where the blue flowers are instead of going left to the exit go right. There's a bunch of flowers under a roof and the secret.



















Secret Flower 3:
The last secret flower is behind the second fan right after you exited the highway.