As part of the NERC funded Shelf Seas Biogeochemistry program, microbial structure, diversity and abundance was compared in four contrasting sediment types, from mud to sand. Samples were collected before (March 2015) and immediately after a spring diatom bloom (May) and also again in late summer (August). These data are 16S rRNA and 18S rRNA gene sequence sets from the four sediment types, and from the three sampling time points. Relative abundance and composition was determined using Illumina MiSeq (MrDNA, TX, USA). The V1V3 region of 16S rRNA was amplified using the PCR primers 27F (Vergin et al., 1998) and 519Rmod (Andreotti et al., 2011) using the PCR and sequencing conditions described in Tait et al. (2015). For 18S rRNA genes, the primers Euk7F and Euk570R were used.