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This paper is the second in a pair investigating potential mechanisms for ecological regime change in salinising wetlands. The first paper in this series focused on the responses of the salt-tolerant submerged macrophyte community to salinity. In this second paper, we investigated some of the environmental conditions required for initiation and dominance of benthic microbial communities using a combination of experimental and observational data. Two experiments were carried out. One investigated the importance of prior establishment of benthic microbial communities on their ability to maintain prevalence over macrophyte colonisation (‘persistence’ experiment), while the other investigated hydrology and its effect on sediment perturbation, potential nutrient release and subsequent benthic microbial community establishment (‘flooding’ experiment). The ‘persistence’ experiment measured the biomass of benthic microbial communities and emergence of macrophytes from sediments kept either wet or dry for 4 weeks then flooded at a range of salinities. Benthic microbial biomass was similar across all of the salinities tested (15, 45 and 70 ppt), with a slight increase at higher salinities, suggesting that none of these limited benthic microbial community development. Pre-wetting of sediments usually increased benthic microbial community biomass and reduced macrophyte germination, but the latter was attributed to the presence of anoxic sediments rather than the increased benthic microbial community biomass. Germinating macrophytes emerged through benthic microbial communities or dense heterotrophic bacterial blooms, demonstrating that they could become dominant even when another community was already established. Field data supported these results, suggesting that the development of benthic microbial communities is not limited by salinity alone, but includes other factors, such as the water regime. In the ‘flooding’ experiment, the largest differences in nutrient concentrations ultimately lay between the pre-wet and pre-dry treatments (due to the greater release of nutrients and development of anoxia in the latter) rather than those subjected to fast versus slow flooding. In response to this, highest benthic microbial community biomass was in treatments with pre-wet sediment, corresponding with lower phytoplankton biomass. [ABSTRACT FROM AUTHOR]