Abstract The West Alboran Basin was previously classified as a mud volcanic province consisting of two mud volcano (MV) fields that are inactive at the present day: the Northern (Spanish) and the Southern (Moroccan) fields. The discovery of the first active mud volcano (Carmen; cruise TTR-17) in 2008, along with several pockmarks at the central part of the basin, motivates more careful geological and geochemical analysis of previous data and comparison to new observations. Gas bubbling from the crater of Carmen MV was observed and recorded using an underwater TV-system and a large TV-grab sample. The gas mainly consisted of methane with less than 1% wetness. However, all sets of homologues up to pentane were detected in the mud breccia of Carmen MV. Both molecular and stable carbon isotopic compositions, and their distribution along the core length, suggest a deep thermogenic source of hydrocarbons (HCs). Composition of the pore water from Carmen MV also points to a deep source of mud volcanic water. The isotopic results indicate that the source of mud volcanic water is the dehydration of clay minerals in the thermal zone of the smectite-to-illite transformation. Our observations allow us to infer the presence of structure II gas hydrates in mud breccia on the top of Carmen MV. High HC gas saturation in sediments in some pockmarks accompanied with live chemosynthetic fauna directly indicates the strong seepage activity of these structures. For the first time, authigenic carbonate crusts and chimneys with associated living chemosynthetic bivalves and tubeworms were sampled from a seep site in the West Alboran Sea. Authigenic carbonates consist of aragonite and calcite, and are characterized by a light carbon isotopic signature, up to −37.2‰ PDB, which points to their methane-derived origin.