The Lithuanian sea space belongs to the smallest sea areas in Europe. The sea space incorporates multiple marine ecosystem services (MES) that support human-wellbeing and sustain maritime economies, but is also subjected to intensive anthropogenic activities that can affect its vulnerable ecological components. We present a flexible geospatial methodology to assess MES richness (MESR) and to analyse areas of exposure of MES to human impacts using a MES exposure index (MESEx). Source of anthropogenic threats to MES were firstly derived from the Marine Strategy Framework Directive and include marine litter (from ports and shipping), underwater noise (from offshore pile driving and shipping) and hazardous substances (from oil extraction platforms). Results were presented for the three main planning areas in Lithuania, the Lithuanian Coastal Stripe, territorial waters and EEZ. In detail, areas of highest MESR are located in the coastal areas of the Lithuanian Mainland Coast that are particularly rich in ecosystem services such as nursery function from for Baltic Herring and cultural services related to valuable recreational resorts, landscape aesthetic values and natural heritage sites. Modelled pressure exposure on selected MES show that cultural ecosystem services in proximity of Klaipėda Port can be particularly affected by marine litter accumulation phenomena, while transboundary effects of potential oil spills from D6-Platform (Kaliningrad Region) can affect valuable fish provisioning areas and coastal cultural values in the Curonian Spit. Results were discussed for the relevance in MES assessment for marine spatial planning in small sea areas and the methodological outlook of the application of geospatial techniques on cumulative impacts assessment within this region of the Baltic Sea.