Moguer is in the southwestern part of the Iberian Peninsula, in the so-called Tierra Llana (“Flatland”) of the province of Huelva. On the north it is bounded by the Río Tinto, the municipalities of Huelva, Niebla and San Juan del Puerto; on the south by the Atlantic Ocean and Palos de la Frontera; on the west by the Río Tinto and Palos de la Frontera; and on the east by Almonte and Lucena del Puerto.
The urban centre of Moguer is located at 19 kilometres from the provincial capital Huelva, and 80 kilometres from the Andalusian capital Seville. It is very close to Palos de la Frontera, and 20 kilometres from the beaches of Mazagón; all of these are within the mancomunidad Moguer-Palos de la Frontera and the larger Comarca Metropolitana de Huelva. Its surface area is 204 square kilometres.