The marine eutrophication (MEu) and marine ecotoxicity (MEc) indicators in Life Cycle Impact Assessment (LCIA) respectively express the eutrophying impact of nitrogen (N) and the toxic impact of metals emissions to the marine environment. Characterisation Factors (CF) are calculated to translate the emissions into impact potentials. For consistency in the characterisation modelling across impact categories, the same modelling framework was applied including Fate Factors of N or metals (FF), habitat Exposure Factor (XF) in MEu or Bioavailability Factor of metals (BF) in MEc, and Factors for the Effect on biota (EF). In both impact categories there is a need for spatial differentiation according to the receiving ecosystems, and the parameterisation of the characterisation models requires the adoption of suitable spatial units out of the global receiving coastal marine ecosystem. The Large Marine Ecosystems (LME) biogeographical classification system identifies 64 spatial units of coastal marine waters and it was adopted for both MEu and MEc. The applicability of 13 alternative zonation systems was compared before choosing the LME classification. The hydraulic residence time (RT) of the receiving LMEs expressing the system’s flushing through local hydrodynamics is required for the parameterisation of the FF term to estimate the loss of N or metals from the LME through advection. The RT was found in literature for 36% of the LMEs, whereas 4 archetypes were built for the remaining, for which no data was found (47%) or to settle high variability of found sources (17%). The 4 archetypes were defined by the exposure to currents and regional marine circulation, depth and profile of the continental shelf, and stratification. Archetype 1 (high dynamics and exposure) with estimated RT=3 months, Archetype 2 (medium dynamics and exposure) with RT=2 yr, Archetype 3 (low dynamics) with RT=25 yr, and Archetype 4 (very low dynamics, embayed, often stratified) with RT=90 yr. It is assumed that the system dynamics is determining the RT of both N and metals in the photic zone in each LME. The LME classification system was chosen for its data availability, modelling feasibility, and adequacy of size and number of spatial units considering the needs of LCIA. The application of the archetypical RTs was useful for the parameterisation of the fate models. The spatial differentiation of the resulting CFs was found essential to increase the discriminatory power of the models.