The spatial dependency of pesticide emissions to air, surface water and groundwater is illustrated and quantified using PestLCI 2.0, an updated and expanded version of PestLCI 1.0. PestLCI is a model capable of estimating pesticide emissions to air, surface water and groundwater for use in life cycle inventory (LCI) modelling of field applications. After calculating the primary distribution of pesticides between crop and soil, specific modules calculate the pesticide’s fate, thus determining the pesticide emission pattern for the application. PestLCI 2.0 was developed to overcome the limitations of the first model version, replacement of fate calculation equations and introducing new modules for macropore flow and effects of tillage. The accompanying pesticide database was expanded, the meteorological and soil databases were extended to include a range of European climatic zones and soil profiles. Environmental emissions calculated by PestLCI 2.0 were compared to results from the risk assessment models SWASH (surface water emissions), FOCUSPEARL (groundwater via matrix leaching) and MACRO (groundwater including macropore flow, only one scenario available) to partially validate the updated model. A case study was carried out to demonstrate the spatial variation of pesticide emission patterns due to dependency on meteorological and soil conditions. Compared to PestLCI 1.0, PestLCI 2.0 calculated lower emissions to surface water and higher emissions to groundwater. Both changes were expected due to new pesticide fate calculation approaches and the inclusion of macropore flow. Differences between the SWASH and FOCUSPEARL and PestLCI 2.0 emission estimates were generally lower than 2 orders of magnitude, with PestLCI generally calculating lower emissions. This is attributed to the LCA approach to quantify average cases, contrasting with the worst-case risk assessment approach inherent to risk assessment. Compared to MACRO, the PestLCI 2.0 estimates for emissions to groundwater were higher, suggesting that PestLCI 2.0 estimates of fractions leached to groundwater may be slightly conservative as a consequence of the chosen macropore modelling approach. The case study showed that the distribution of pesticide emissions between environmental compartments strongly depends on local climate and soil characteristics. PestLCI 2.0 is partly validated in this paper. Judging from the validation data and case study, PestLCI 2.0 is a pesticide emission model in acceptable accordance with both state-of-the-art pesticide risk assessment models. The case study underlines that the common pesticide emission estimation practice in LCI may lead to misestimating the toxicity impacts of pesticide use in LCA.