Sediment deposition is known to affect the structure of marine rocky-bottom communities, but its specific effects on some key organisms, such as sponges, remain poorly investigated. In a 125-day field experiment involving different treatments of exposure to sediment deposition, we investigated survival of asexually produced recruits of the sublittoral demosponge Scopalina lophyropoda, a model organism suitable to understand similar processes in other sponges. A total of 660 explants obtained from 11 non-clonal sponges (explant donors) were distributed on 30 experimental plates. Each donor sponge contributed two clonal explants per plate, one settled under a roof at a silt-protected position and the other at a silt-exposed position. Plates were installed at the rocky walls of the natural community, also at the pillars of a local harbor where the sponge does not occur naturally. A 3-way ANOVA testing for differences in explant longevity as a function of explant donor, exposure to sediment, and habitat detected that longevity was affected by both an undetermined genetic condition of the explant donor and exposure to silt. Silt-protected explants lived longer than silt-exposed explants. A significant “Silt-exposure × Habitat” interaction detected that silt-exposed explants lived shorter within the harbor than in the natural community, suggesting that harbor silt, which was notably finer, is more deleterious. Inspection of daily mortality rates revealed that the detrimental effects of silt were very evident during the first 20 days in treatments and irrespective of habitat. Then, mortality rates progressively decreased, reaching negligible values in all 4 sponge groups by day 65. At this stage, an undetermined mortality factor other than purely sediment deposition reactivated mortality in all 4 sponge groups, but it affected more intensely the sponges in the harbor, irrespective of being protected from or exposed to sediment deposition. All together, the results of our field experiment suggest that sediment loads are a major mortality factor among small sponge individuals in sublittoral rocky communities. Because a significant “donor factor” suggests an unidentified “genetic component” to be involved in the ability to cope with sediment, natural or man-driven processes increasing coastal sediment deposition are susceptible to induce changes not only in the abundance but also the genetic structure of the sponge populations in the long term.