The geological storage of carbon dioxide (CO2), captured from large industries and power plants, is expected to be an important component of future carbon emissions mitigation globally. Alongside the need to understand the impacts of a CO2 leak on the marine environment, there is an urgent need to develop monitoring protocols for leakage detection. In the present study, sediment cores were exposed to seawater acidified using CO2 to five different pH levels (8.0, 7.5, 7.0, 6.5 and 6) for a period of 10 weeks. A pink microphytobenthos mat containing Spirulina sp. and diatoms appeared on top of sediment exposed to pH 7.0 and 7.5 after five weeks, peaked at eight weeks and was still present in small patches within the pH 7.0 cores after 10 weeks. Quantitative PCR measurements of the abundance of cyanobacterial 16S rRNA also indicated an increase to the abundance of cyanobacterial or chloroplast 16S rRNA within the pH 7.0 treatments after 10 weeks incubation. Detailed comparisons of the microbial communities with the pH 7.0, 7.5 and 8 treatments revealed a shift in community composition within the pH 7.0 cores: an increase in abundance of sequence most closely related to Spirulina sp. and the diatom Navicula sp., and a corresponding decrease to the abundance of Alphaproteobacteria, specifically of the family Rhodospirillales, the Crenarchaeota Class Marine Group I and the Planctomycetes Class OM190. Monitoring for blooms of microphytobenthos may prove useful as an indicator of a CO2 leak from injection pipeline failure in coastal areas.