Bacterial pathogens are a major cause of economic losses in cultured fish production worldwide; yet the reservoirs of such pathogens in the natural environment are poorly understood. We hypothesised that microorganisms could attach to aquatic aggregates (such as marine snow) before settling to the seabed, where they may persist as viable organisms for some time. This study aimed to 1) understand the interactions of disease-causing organisms in the water column above sediments colonised by biofilms and 2) predict the fate and transport of those pathogens using flume experiments. Using 16S rRNA gene metabarcoding, we detected potential sequences from human-associated (Mycobacterium) and fish associated (Tenacibaculum) pathogens in sediments of aquaculture and non-aquaculture sites. In controlled flume studies, all the target organisms (Tenacibaculum maritimum, Enterococcus faecium and bacteriophage P22) decayed more slowly in sediments than in the open water, suggesting that sediments can act as reservoirs of aquaculture-related pathogens, potentially threatening aquatic and human health. The longer decay rates of aggregate-bound cells in both stationary microcosms and continuous-flow flume experiments revealed that marine snow could serve as vectors to facilitate microbial survival and persistence. The outcomes of this study may help to inform future aquaculture operations of their environmental impacts and improve safe aquaculture farming practices and food security.