Drizzle olive oil over the bottom of a large soup pot. Turn heat to medium-high. Add the diced onion to the olive oil and saute for 4 minutes. Then add the minced garlic and saute for 1 more minute.
Add the lentils and water to the pot. Raise the temperature to high. Bring the water to a boil. Place the lid on the pot tilted, lower the heat, and simmer for 10 minutes.
Add the vegetable broth, carrots, celery, bell pepper, jalapeno pepper, and diced tomatoes to the pot. Stir in the thyme, marjoram, cumin, and red pepper flakes. Raise the heat to high and bring the soup to a boil. Once the soup reaches a boil, lower the temperature to medium, but make sure the soup continues at a low boil.
Cook for 10 minutes or until the carrots are fork-tender.