Triploidization is currently the preferred method to induce sterility in finfish aquaculture, to improve production and mitigate the effects of escapees interbreeding with wild conspecifics. However, triploid Atlantic salmon (Salmo salar) occasionally exhibit poor performance and welfare compared to diploids, the reasons for which are not fully understood. Having previously identified genetic aberrations among supposedly triploid salmon produced using a hydrostatic pressure-shock, we hypothesized that unexpected drops in hydrostatic pressure could induce 'failed-triploidy' and explain poor performance and welfare. To test this, we subjected Atlantic salmon eggs from three half-sibling families to five hydrostatic pressure treatments: a diploid control (0 PSI), three suboptimal pressures, 44.82, 51.71, 58.61 MPa (6500, 7500, and 8500 PSI), and a triploid control 65.50 MPa (9500 PSI). We monitored their growth and welfare throughout a 2.5-year production cycle and x-rayed a subsample of fish at harvest. Fish performance and welfare were primarily driven by ploidy and family effects, with differences among groups becoming evident after seawater transfer. Fish from certain half-sibling families performed particularly poorly as triploids, either through high mortality, poor growth and welfare, or a higher incidence and severity of vertebral deformities. There was limited evidence for sub-optimal pressure treatments themselves causing growth and welfare concerns. We conclude that, although sub-optimal pressure treatments can increase the number of non-viable offspring caused by inheritance aberrations, the performance of surviving fish is dictated by an interaction between ploidy and family effects. Selective breeding tailored to the triploid state therefore has the potential to improve triploid performance.