Nitrogen (N) fertilisation has positive and negative effects on the environmental impact of crop cultivation. The mechanisms governing these effects are highly site-dependent, a factor often ignored in assessments of the environmental impact of crop cultivation. By assessing outputs of crop rotations using a life cycle approach, this study explored how greenhouse gas emissions and marine eutrophication caused by crop cultivation (including upstream processes such as production of farm inputs) depend on fertiliser rate and the site at which the cultivation occurs. Cereal unit (CU) was used as the functional unit. The calculations were based on data from multi-site long-term field experiments in Sweden and site-dependent data and models for non-measured processes. Cultivation at three N levels was evaluated, where the highest N rate was close to current average practices and the lowest level corresponded to one-third of that. Site characteristics had a stronger influence on both greenhouse gas emissions and marine eutrophication (variations of up to 330% and 490%, respectively, within N levels) than N level (variations of up to 74% and 59%, respectively, within sites). Main sources of variation in greenhouse gas emissions were soil nitrous oxide emissions (58–810 g CO2eq CU−1) and soil organic carbon changes (14–720 g CO2eq CU−1), while variations in marine eutrophication were mainly explained by field-level waterborne N losses (0.9–8.2 g Neq CU−1). The large variation between sites highlights the importance of considering site characteristics when assessing the environmental impact of crop cultivation and evaluating the environmental consequences of crop management practices.