We investigated meiobenthic community response (as density and vertical distribution) to the sedimentation of phytoplankton in 2 contrasting sites in the southern North Sea, one with fine grained sediment close to the coastline and another with highly permeable sediments. Meiobenthic densities and pigments in the water column and sediment were measured monthly from October 2002 until October 2003. Stable isotope 13C and 15N signatures were analysed in sediment particulate organic matter (POM), water suspended particulate matter (SPM) and in different meiobenthic taxa at 3 different times (prior, during and after spring bloom deposition) at 2 sediment depths (0 to 1 and 4 to 5 cm). Our aim was to determine whether sediment type affects the overall meiobenthic community response (densities and vertical distribution) and utilisation of freshly deposited phytoplankton as a food source. Variation in nematode response to the sedimentation event was evident and was related to the contrasting biogeochemical processes at the stations. In permeable sediments, the nematode response was rapid after phytoplankton deposition, while in the fine-grained station, nematode response (as density) was delayed. In general, meiobenthic 13C signatures remained relatively constant over time and were not coupled with changes in water SPM and sediment POM. There was vertical variation in meiobenthic 13C signatures in fine sediments. Nematodes belonging to the genera Sabatieria and Richtersia from the deeper sediment layer had isotope signatures similar to those of surface living nematodes, indicating migration of these genera to the surface to feed. In permeable sediments, such vertical differences were absent because of sediment biogeochemical properties. δ13C and δ15N values of copepods clearly indicated a chemoautotrophic food source within the fine-grained sediment, which has not been previously reported for these environments.