Remember: All the flowers are pink! And you need to press the use button to collect them! Now then...

mimp1 (First map)
When you reach the garage building with the yellow car, go towards the small tunnel you came from without jumping down from the short cliff. You'll find the first flower, seemingly glowing.

mimp2 (Third map, the one after the intermission map. Intermission map has no flowers)
When you get to the gas station, go to the right side of the road towards the cliff, and look for a way down. You'll find some stairs that lead to a narrow path, leading to the flower next to a doorway to an inaccessible building.

mimp3 (Fourth and final map)
After you cross a small railroad inside the Combine structure, you're reach a Xen-like habitat with alien plants and giant 'eggs'. Before crossing the bridge to reach the next part of the level, look for a ladder and climb down. Walk through the foliage and towards the far end to find the last flower.

After you find them all, you need only to finish the game!