The field of marine microbial ecology of eukaryotes started to flourish due to large scale projects and new methodological innovations in molecular ecology and genomics. In line, functional analysis of marine microeukaryotic communities that combine biodiversity patterns and metatranscriptome profiles to define taxon-specific activities are only recently emerging. We will present a comprehensive dataset that links abiotic measurements to microeukaryotic community composition and its respective metatranscriptome profiles. The analysis of our metatranscriptome profiles was enabled due to the Marine Microbial Eukaryotic Transcriptome Sequencing Project (MMETSP). Specifically we will show how diversity and taxon-specific transcription patterns change within and between different ecosystems. Our data are derived from I) Disko Bay, an Arctic ecosystem located at the west coast of Greenland (69°N), II) North Atlantic waters influenced by the Gulf Stream around the islands of the Lofoten at the west coast of Norway (68/69°N) and III) a mixed water body ecosystem (North Sea / Baltic Sea) in the Kattegat around the island of Orust (58°N), located at the west coast of Sweden. Each ecosystem is represented by 5 different sampling stations. Abiotic environmental measurements contain temperature, salinity, chlorophyll, macronutrients (N and P) and silica. Molecular diversity was assessed via amplicon sequencing of the 28s hypervariable D1/D2 region with the 454 technology. Metatranscriptomic data was obtained with RNAseq using the Illumina 100 paired-end technologies.