Benthic species and communities are linked to pelagic zooplankton through life-stages encompassing both benthic and pelagic habitats and through a mutual dependency on primary producers as a food source. Many zooplankton taxa contribute to the sedimentary system as benthic eggs. Our main aim was to investigate the nature of the population level biotic interactions between and within these two seemingly independent communities, both dependent on the pelagic primary production, while simultaneously accounting for environmental drivers (salinity, temperature and oxygen conditions). To this end we applied multivariate autoregressive state-space models to long (1966–2007) time-series of annual abundance data, comparing models with and without interspecific interactions, as well as models with and without environmental variables included. We were not able to detect any direct coupling between sediment-dwelling benthic taxa and pelagic copepods and cladocerans on the annual scale, but the most parsimonious model indicated that interactions within the benthic community are important. There were also positive residual correlations between the copepods and cladocerans potentially reflecting the availability of a shared resource or similar seasonal dependence, whereas both groups tended to correlate negatively with the zoobenthic taxa. The most notable single interaction within the benthic community was a tendency for a negative effect of Limecola balthica on the amphipods Monoporeia affinis and Pontoporeia femorata, which can help explain the observed decrease of amphipods due to increased competitive interference.

The data consist of field data on zooplankton abundances gathered during 2016, as well as the time-series used for the community model described in the paper.