Purpose Integrated multi-trophic aquaculture (IMTA), growing different species in the same space, is a technology that may help manage the environmental impacts of coastal aquaculture. Nutrient discharges to seawater from monoculture aquaculture are conceptually minimized in IMTA, while expanding the farm economic base. In this study, we investigate the environmental trade-offs for a small-to-medium enterprise (SME) considering a shift from monoculture towards IMTA production of marine fish. Methods A comparative life cycle assessment (LCA), including uncertainty analysis, was implemented for an aquaculture SME in Italy. Quantification and simultaneous propagation of uncertainty of inventory data and uncertainty due to the choice of allocation method were combined with dependent sampling to account for relative uncertainties and statistical testing and interpretation to understand the uncertainty analysis results. Monte Carlo simulations were used as a propagation method. The environmental impacts per kilo of fish produced in monoculture and in IMTA were compared. Twelve impact categories were considered. The comparison is first made excluding uncertainty (deterministic LCA) and then accounting for uncertainties. Results and discussion Deterministic LCA results evidence marginal differences between the impacts of IMTA and monoculture fish production. IMTA performs better on all impacts studied. However, statistical testing and interpretation of the uncertainty analysis results showed that only mean impacts for climate change are significantly different for both productive systems, favoring IMTA. For the case study, technical variables such as scales of production of the species from different trophic levels, their integration (space and time), and the choice of species determine the trade-offs. Also, LCA methodological choices such as that for an allocation method and the treatment of relative uncertainties were determinant in the comparison of environmental trade-offs. Conclusions The case study showed that environmental trade-offs between monoculture and IMTA fish production depend on technical variables and methodological choices. The combination of statistical methods to quantify, propagate, and interpret uncertainty was successfully tested. This approach supports more robust environmental trade-off assessments between alternatives in LCAs with uncertainty analysis by adding information on the significance of results. It was difficult to establish whether IMTA does bring benefits given