Professor Neil Frazer of the Department of Geology and Geophysics at the University of Hawaii at Manoa explains how farm fish cause nearby wild fish to decline. In his paper he wrote that higher density of fish promotes infection, and infection lowers the fitness of the fish. He told that for wild fish, lowered fitness means more difficulty finding food and escaping predators, causing higher death rates.
Besides feeding the farmed fish are also protected from predators by their cage, so infected farm fish live on, shedding pathogen into the water. The higher levels of pathogen in the water cause the death rates of wild fish to rise. Frazer said that sea lice are an important example of disease transfer in ocean fish farming. Sea lice are tiny crabs that attach to marine fishes, eating their skin and sometimes deeper tissue. Skin is important to fish because they need to keep their tissues less salty than the ocean.
Frazer also continued saying that after lice puncture the skin they create an entry point for other infections. So wild fish weakened by lice have more difficulty finding food and escaping predators. Larger numbers of lice are especially dire for salmon because juvenile salmon must transit coastal areas where salmon farms are located.