Salt marshes are very important areas for biogeochemical cycling, sediment accretion, pollution filtration and retention and erosion and stabilization of the river margins. The high organic matter content in the salt marsh plant sediments along with the radial oxygen diffusion provided by these halophyte root systems gather the ideal conditions for the development of a microbial rhizosphere community. Due to the quick feedback of the microbial communities to an environmental change, these organisms become important monitors for environmental impact assessment. A Salt marsh Sediment Microbial Index (SSMI) that reflected physical–chemical and microbial parameters was applied to plant rhizosphere sediments of five salt marshes from three important water bodies from Portugal. The SSMI revealed to be plant-independent evaluating efficiently the different marshes according to their maturity degree and disturbance influence. Mature salt marshes SSMI classification grouped all the systems at this development stage, while the younger salt marshes are classified in different groups according to their evolution degree. Also the impact degree is reflected at this level discriminating also the more adversely impacted salt marshes. Being a multi-metric index, the SSMI sub-metrics are also susceptible of ecological interpretation, giving important backstage information about the underlying biogeochemical cycling processes.