Bring water to a boil in a Dutch oven. Stir in the couscous and salt and cook until tender, about 5 minutes. Drain the couscous, transfer to a large bowl, and cover to keep warm.

Wipe the pot dry, add a portion of the oil, and set over medium-low heat until the oil shimmers. Add the fennel, onion, and salt; cover and cook, stirring occasionally, until the vegetables have softened and released their liquid, about 15 minutes.

Uncover the pot, increase the heat to medium-high, and cook until the liquid has evaporated and the vegetables are lightly browned, 15 to 20 minutes—stir often during this stage to prevent sticking.

Stir in the garlic and lemon zest and cook until fragrant. Remove the pot from the heat, stir in the spinach, and cover until the leaves are wilted, about 2 minutes.

Fold in the cooked couscous, lemon juice, chives, and the remaining oil. Season with salt and pepper to taste and serve warm or at room temperature.