Myotis capaccinii hunts by trawling over smooth water surfaces of rivers, but also lakes and ponds, preferring sites with abundant food, mostly chironomids and other small nematocerans, but the diet varies much according to the study region; piscivory is also known for Iberia, Italy, and Israel. The bats mostly move following watercourses and forage within a range of 7-15 km (up to ca. 31 km) around the roost (reviewed in Aihartza and Aizpurua, in press), at least in Italy showing preferences over well-preserved riparian vegetation and high-water quality. This species roosts year-round in natural or artificial underground sites, and is a regional migrant, with seasonal moves between summer and winter quarters of 40-50 km (Hutterer et al. 2005).

Myotis capaccinii is a mostly Mediterranean species occurring in the lowlands, from Spain east to Italy, the Balkan Peninsula, Romania, Bulgaria and the western coasts of the Black Sea. To the north, its distribution is mostly limited by the Alps and by the Transylvanian Alps in the Eastern Balkans (reviewed in Aihartza and Aizpurua, in press). Previously reported for the Spanish territory of Ceuta, in North Africa, yet its presence was not confirmed by López-Baucells et al. (2012) and no further, more recent data are available. Present on Mediterranean islands, including the Balearic Islands, Sardinia, Corsica, Sicily, Crete, Zakynthos and Petalas. The range of altitudes where this species can be found varies between 0 and 1,500 m asl. The AOO was estimated using 2x2 km grid cells. The species was last recorded with certainty in Switzerland in the early twentieth century (Aihartza and Aizpurua, in press), and it is considered possibly extinct in both Switzerland and in the Spanish North African territories (not mapped).

Outside Europe, the species occurs along the Mediterranean coast of northwestern Africa and in Türkiye, Syria, Lebanon, Palestine, Israel, and Jordan, and follows the Euphrates River across Iraq and through Iran, possibly to Uzbekistan (Aihartza and Aizpurua, in press).

Myotis capaccinii is protected by national legislation in most range states. There are also international legal obligations for its protection through the Eurobats Agreement and Bern Convention. It is included in Annexes II and IV of 92/43/EEC Habitats Directive, hence requiring special measures for conservation including the designation of Special Areas for Conservation. 481 Natura 2000 sites include this species in their designations (EEA 2023). According to art. 17 reporting made within the framework of the above-mentioned Habitats Directive for years 2013-2018, the conservation status in the EU is unfavourable-inadequate. The survival of this species is closely tied to the health of rivers and the quality of riparian habitats. Therefore, it is essential to ensure the strict protection of riparian vegetation and maintain high water quality standards. In addition, the underground sites where the species roosts must be safeguarded from potential threats, such as speleologists, and not be exploited for tourism purposes.