<p>Intact sediment cores serving as mesocosms are characterised by the actual three-dimensional distribution of animal and plant communities, as well as the zonation of various processes in the vertical profile. However, neither their collection in the field nor subsequent preparation for experiments has been well developed. Intact soft bottom cores for experimental purposes can be collected by any soft-sediment sampler with a transparent sampling tube detachable from the sampler head. The sampling tubes can serve as both a coring device and a mesocosm container, as shown in this article and exemplified by the use of the HAPS DK bottom core. Because the tubes are replaceable, the number of units is not limited in principle and should be adjusted to the required number of treatments and replicates. Simple instrumentation was developed in the scope of the study that allows for the collected sediment to be placed at the same adjustable height in all tubes (to minimise potential hydrodynamic bias), and for slicing the cores after the experiment for further biological and/or chemical analyses. The described system has been successfully used to study the burrowing behaviour of clams in various sediments and seasons.</p>