The objective of this work was to determine the effects and implications of generic and site-specific aquatic eutrophication potential indicators in the Life Cycle Assessment (LCA) of livestock farm systems using a New Zealand (NZ) lake catchment case study. Average dairy and sheep & beef farm systems in the Lake Taupo catchment were studied. Emissions of nitrogen (N) and phosphorus (P) to waterways, and ammonia and nitrogen oxides to air from these farms were calculated using the site-specific OVERSEER® nutrient budget model. These emissions data were then used to calculate the increase in nutrients in water bodies and aquatic Eutrophication indicators with a range of Life Cycle Impact Assessment (LCIA) methods. Eutrophication indicator results varied considerably depending on the environmental mechanisms modelled by the LCIA method for the fate of N and P, accentuated by different choices for the inventory modelling. Using default emission factors instead of site-specific ones overestimated eutrophication impact results. The most recent methods are not only spatially-explicit and applicable beyond Europe, but they also account for more environmental mechanisms for the fate of the nutrients, giving relatively lower calculated impact results. However, the appropriate scale and spatial resolution is still a crucial question to address for these methods since they greatly affect results. Regarding eutrophication damage assessment, when the actual background nutrient concentration is very low, the end-point assessment method for freshwater eutrophication is not applicable. In this case, LCA fails to account for a high standard of water quality that is in a near-pristine state, but deteriorating. The inventory of nutrient flows at a farm scale and fate factors modelled at a catchment scale should be site-specific. Freshwater eutrophication indicators should be based on a site-specific (and globally-valid) LCIA model rather than a generic one. Currently-accepted freshwater eutrophication indicators focus only on P, thus capturing only part of the problem for freshwater bodies that are co-limited by N and P (in terms of algal growth) such as Lake Taupo in NZ. Lake Taupo water quality concerns and regulations are not focused on P, but solely on N due to increasing N levels over time. Conclusions from this study are valid beyond NZ and beyond agricultural systems. Future work needs to investigate coupling N and P fate modelling based on the most recent globally-valid and spatially-explicit LCIA methods. Display omitted •Eutrophication impact results varied considerably depending on the LCIA method.•Default emissions factors instead of site-specific ones overestimated impacts.•Eutrophication indicators focusing on one nutrient may not be relevant.•Freshwaters can be limited by N and P as shown here for New Zealand.•P effect modelling fails to account for high water quality standards and policy.