In the last few years, the endemic Mediterranean bivalve Pinna nobilis has been exposed to dramatic mortality in its entire area, which could lead to the extinction of the species. Throughout the Mediterranean, a lot of effort is being put into finding ways of preserving it. One of the methods used to monitor recruitment and juveniles’ survival is the installation of collectors for bivalve larvae. We installed collectors at two locations: in Brijuni National Park (North Adriatic) and Luka Cove (central Adriatic). Our aim was to compare the fouling community on the collectors in two consecutive years (2019 and 2020), especially because the installation of collectors in 2020 coincided with mass mortality events of P. nobilis in the area. The number and size of juvenile P. nobilis and the qualitative and quantitative composition of the fouling communities were determined. The results show a reduction in the number and size of juvenile P. nobilis and an explosion of the invasive bivalve Anadara transversa population on collectors in the second year. In Luka Cove, another invasive species—the ascidian Styela plicata—also seriously affected other organisms on the collectors to the point of preventing analysis of the fouling community.