The main goal of the study was to follow the colonization process of soft-bottom macrofauna commu- nities in two wetland systems with different organic inputs: a lagoon reservoir and a fish-farm system in the Ria Formosa, Portugal. After a previous treatment in the natural sediments, the resulting experimental azoic sediments were placed in suspended boxes. Two sets of boxes were used to study seven cumulative colonization periods of increasing duration, and seven colonization periods of one month each. Community structure was studied and percentage of organic matter in surface sediments was measured. Descriptors of the macrozoobenthic community included abundance, density, number of species, and diversity, dominance and evenness indices for polychaete taxa. Significant differences were observed in the community structure between colonization periods and between systems. Cumulative experiments revealed that organic enrichment is associated with sediment colonization which is marked by a macroinvertebrate community of increasing total abundance of settlers and diversity in the reser- voir, and several peaks for abundance of a few opportunistic polychaete species in the fish-farm which is typical of a highly disturbed system. Comparison of experimental and natural bottom sediments revealed that predation and organic inputs are important factors determining the community structure, for density in the case of predation and diversity in the case of organic loads. We observed that the duration of the colonization period is a key factor in the community structure of the less disturbed system, as shown by the higher diversity in bottom sediments of reservoir.