At least 275 non-indigenous species (NIS) have been reported in the ecoregion with the earliest records dating to the year 1700. The rate of NIS detections has been increasing since the 1970s, corresponding with increased awareness and research effort. Nine new NIS were detected in the ecoregion during 2016–2018, however, the data for the most recent decade are likely incomplete because of a lag between the actual date of an NIS' introduction and the collection, identification and reporting of the species.
The southernmost part of the ecoregion, the Gulf of Cadiz, can be considered an NIS hotspot, exhibiting an accelerated recent invasion of such species. This may have been influenced by recent anthropogenic alteration of the habitat and facilitated by climate change through supporting the spread of warm‑water NIS.
In general, the ecological impacts of NIS in the marine realm are poorly quantified. In this ecoregion, the decline of native species and structural changes in its benthic communities as a result of NIS introductions have been recorded. Other effects include the fouling of irrigation systems and clogging of fishing gear and aquaculture facilities.