Fish capture in industrial aquaculture is both necessary (i.e., for transfer, monitoring and harvesting) and difficult. The most logistically feasible methods rely heavily on crowding, a process that is detrimental to fish welfare and production outcomes. Jump nets, which rely on passive capture via jumping behaviour, present a welfare-friendly alternative. But reliance on behaviour means capture is not guaranteed, and limited knowledge of their capture rate and sampling biases means they are not yet used to their full potential. Here, in sea-cages stocked with Atlantic salmon Salmo salar, we investigated how capture rate varied with net size, position, and time of day, and if salmon caught via jump net were representative of the sea-cage population. A comparison of jumping rates into surface rings (without nets) indicated that larger jump nets will catch more fish. Capture rate was highest in rings positioned in the centre of cages, and during the morning and evening. Jump nets sampled representatively for fish size but caught salmon with marginally lower condition (<2% difference) and with three times higher parasitic salmon louse (Lepeophtheirus salmonis) loads than fish caught using lift nets. Our results indicate that jump nets can be used as a size-representative sampling tool and to target lice infected salmon for treatment.