Microbial activity within the environment can have distinct geochemical effects, and so changes in a microbial community structure can result in geochemical change. We examined seasonal changes in both the microbial community and the geochemistry of an inter-tidal salt marsh in northwest England to characterise biogeochemical processes occurring at this site. Phospholipid fatty acid (PLFA) analysis of sediment samples collected at monthly intervals was used to measure seasonal changes in microbial biomass and community structure. The PLFA data were analysed using multivariate techniques (Ward's method and the Mahalanobis distance metric), and we show that the use of the Mahalanobis distance metric improves the statistical analysis by providing detailed information on the reasons samples cluster together and identifying the distinguishing features between the separate clusters. Five clusters of like samples were defined, showing differences in the community structure over the course of a year. At all times, the microbial community was dominated by PLFA associated with aerobic bacteria, but this was most pronounced in summer (August). The abundance of branched fatty acids, a measure of the biomass of anaerobes, started to increase later in the year than did those associated with aerobes and the fungal biomarker 18:2ω6 showed a brief late-summer peak. The salt marsh remained mildly oxic throughout the year despite the increase in microbial respiration, suggested by the large increases in the abundance of PLFA, in the warmer months. The conditions therefore remained most favourable for aerobic species throughout the year, explaining their continual dominance at this site. However, as the abundance of PLFA synthesised by anaerobes increased, increases in dissolved Mn concentrations were observed, which we suggest were due to anaerobic respiration of Mn(IV) to Mn(II). Overall, the geochemical conditions were consistent with the microbial community structure and changes within it.