The bishopric of Ampurias, also known as Diocese of Flumen ('the stream' in Latin), was founded circa 1170, like the Diocese of Gallura (later renamed Civita), plausibly when Pope Alexander II reorganized the ecclesiastical jurisdictions of Sardinia, which was being temporally divided into four autonomous giudicati ('judgedoms'), corresponding to the administrative curatorial of Anglona in the Giudicato of Torres, as suffragan of the Metropolitan Archdiocese of Torres.
Its original episcopal see, Amurias, was an Ancient port town, presumably at the coast of Codaruìna near Valledoria by the bay of Coghinas.
The first historically recorded Bishop of Ampurias, Bono, had a part around 1100 in the foundation of the monastery of San Nicolò di Solio, one of many founded in the diocese by the Cassinese Benedictine Congregation in the 11th and 12th centuries, thirteen of which depended on Santa Maria di Tergu; whether their possessions ware exempt from the episcopal authority remained a matter of continuous dispute, giving to several papal interventions in favor of the Benedictines, possibly culminating in the murder of the abbot of Santa Maria di Tergu shortly before 1203.
The town of Ampurias faded with its port due to the sand-clogged bay of Coghinas, so in the 14th century the episcopal see was effectively transferred (without title change) to Castelgenovese (now Castelsardo), formalized in 1503 when Pope Julius II elevated the Benedictine priory of Sant'Antonio into the new diocesan cathedral, which presently remains co-cathedral in the successor bishopric.
From 1506, the see of Ampurias was held in personal union (aeque principaliter) with the Diocese of Civita, until they merged effectively on 1986.09.30, both formally being suppressed in favor of the (present) Diocese of Tempio–Ampurias (with cathedral see at Tempio Pausania, in former Civita) as suffragan of the Metropolitan Archdiocese of Sassari.