System analysis was performed to gain an overview of key environmental challenges and pinpoint hotspots causing environmental impacts in three European food supply chains. An overview was obtained based on a review on LCA studies for beef, dairy, orange juice and aquaculture food supply chains. Similarities of the main environmental impacts were identified to rationalize and justify the selection of key performance indicators chosen for a simplified web based LCA tool developed within the EC funded project SENSE (FP7). Life Cycle Assessment methodology covered many of the key challenges identified but will not be sufficient to address all environmental impacts generated from the food supply chains. Especially for aquaculture impacts that are not taken into account with LCA are i.e. nutrient and organic matter releases, impacts associated with feed provision, diseases introduction, escapes, and changed usage of coastal areas. In agriculture land use and biodiversity are issues not well covered.