This study describes bacterial and eukaryotic communities in estuarine sediments with a range of metal and organic enrichment levels using the universal 16S and 18S genes. Samples were collected from a manipulative field experiment. In addition, both total (DNA) and active (RNA) communities were sequenced. The aim of this study was to investigate the combined impact of metals and organic enrichment on microbial communities and to highlight the applicability of next-generation sequencing techniques for biomonitoring.