Combine the squash, water, stock, and lotus seeds in a medium stockpot. Bring to a boil. Reduce to a simmer, and cook, covered, until squash and lotus seeds are tender, 40 minutes to 1 hour. Season with salt.
Meanwhile, in a small skillet over medium heat, toast the pine nuts until golden brown and fragrant, 5 to 10 minutes. Remove from heat and let stand until cool. Add toasted pine nuts to soup.
Using an immersion blender, puree soup. Alternatively, working in batches, puree in a blender. Serve hot, garnished with scallion.