Large-scale/high-resolution integrated marine ecological information systems combine diverse ecological and environmental data with high resolution in space, time and ecological structure (biodiversity, trophic relationships etc.). This holistic approach opens new ways for analysing and modeling ecological patterns and processes and creates a platform for the development and the application of advanced management and conservation tools. Within the North Sea benthic system, species occurrence patterns and benthic processes are shaped and changed by natural and anthropogenic drivers. Knowledge on species or group specific “natural corridors of variation” in space and time are important to discriminate anthropogenic effects from natural background variability, particularly as the benthos contributes to numerous ecosystem goods and services (biodiversity, food resources etc.). Rare and endangered species play a crucial role in maintaining biodiversity of benthic systems. In 2013, the “red list”, the status of endangered species in German waters, was revised and published. Regrettably, the red list classification of marine benthic species often lacks a scientifically sound foundation, due to insufficient occurrence data. We use an extensive information system on benthic invertebrates in the German North Sea (>9000 stations x >740 species) for analysis of occurrence and spatial distribution of benthic species. We evaluate (a) how rare “red listed” species really are, (b) their spatial distribution, and (c) their functional role in the system by their biological traits. Our ‘red list’ case study shows that large-scale/high-resolution information systems constitute a sound scientific base for improved monitoring assessments and ultimately for a sustainable ecosystem management.