The commune of Mauléon lies within the broader region known as the Pyrenees, forming part of the sub-Pyrenean foothills. From a stratigraphic point of view, the oldest materials outcropping in this area are the variegated clays of the Kauper (there are two small outcrops on the left bank of the Gave de Mauléon or Saison (Uhaitzandi), near Licharre), whose outcrops are always linked to tectonic features (the Roquiague diapiric structure). However, the most characteristic formation is the Cretaceous flysch, and it is necessary to distinguish two sharply contrasting facies. Apart from the flysch outcrops, at the eastern end of the commune (Chéraute anticline) there is a small outcrop of Albian marls which occasionally contain conglomeratic intercalations. The upper part of this formation transitions laterally and vertically into the Mixe flysch. This transition occurs either through the gradual appearance of sandy and silty layers or through the appearance of polygenic conglomerate boulders. The Mixe flysch (Albian–Cenomanian) consists of alternating black and/or ochre-coloured clays and sandstones (Beyrie syncline and Chéraute anticline). Laterally, the Mixe flysch gives way to an alternation of clay, sandstone and limestone lenses with flint (Cenomanian), as observed in the Beyrie syncline and the Roquiague diapir. Finally, in the Gave de Mauléon valley, alluvial deposits are observed that have been dated to the Riss and Wurm periods. Structurally, the folds follow a WNW-ESE direction, parallel to the general orientation of the Pyrenean range. This pattern is disrupted only by the Roquiague diapir.
The lithological homogeneity and low strength of the materials comprising this area give rise to a landscape of monotonous hills that rarely exceed 450 metres (Tibarene, 484 m; Matalon, 439 m). These hills form a series of ridges running ESE-WNO, separated by small valleys of varying widths running NNE-SSW. The low resistance of the Albenses marl has led to the formation of a series of fairly narrow, elongated depressions running ESE-WES, as can be seen in the Chéraute valley or the Roquiague basin.
The river Saison (Uhaitzandi) flows through the commune of Mauléon, passing through the town centre. The river crosses the commune from south to north and, once outside the historical boundaries of the French Basque Country, joins the Gave d’Oloron, which in turn flows into the Adour, which empties into the Atlantic. The river is snow- and rain-fed and is formed by the confluence of various streams in the upper reaches of Zuberoa, from where it receives its snowmelt, as the commune has a maximum altitude of 559 m in the south.
The climate is oceanic, with abundant rainfall throughout the year, peaking in autumn and winter. Annual rainfall is estimated at 1,400 mm, with very few days of snow. Temperatures are moderate throughout the year, with highs in July and August and lows in January and February. The temperature range is around 10–12 °C.