Heat olive oil in a large, deep skillet over medium heat. Add onion and garlic; cook and stir until onion is translucent, about 5 minutes. Season with salt and pepper. Squeeze lemon juice over the onions and add rind in the skillet. Fill the skillet halfway with water; stir in miso paste and vegetable bouillon cube.
Place salmon fillet skin-side down in the skillet. Pour in enough water to cover and bring to a simmer, about 4 minutes. Add baby bok choy, carrots, and celery. Continue simmering until salmon flakes easily with a fork, 2 to 6 minutes more.
Transfer salmon fillets to shallow bowls. Remove lemon rind from the skillet and stir enoki mushrooms, watercress, and green onions into the broth. Cook until heated through, about 20 seconds.
Arrange baby bok choy, carrots, celery, enoki mushrooms, watercress, and green onions around salmon in the bowls. Ladle broth on top.