The impact of petrochemical special economic zone activities on the health status of Jafari Creek was studied by assessing the changes in macroinvertebrate assemblages in nine sites during September 2006–January 2008. The relationship between spatial pattern of macroinvertebrate assemblages and ambient factors (i.e. water temperature, salinity, pH, dissolved oxygen, sediment grain size distribution, sediment organic content, heavy metals contents) was measured. Background enrichment indices, contamination factor and contamination degree, were used to assess the health status in the study area based on nickel, lead, cadmium and mercury contents of the sediments. The macrobenthic communities had a low diversity and were dominated by opportunistic taxa. The BIO-ENV analysis identified salinity, dissolved oxygen, pH and silt/clay content of sediments as the major environmental variables influencing the infaunal pattern. This suggests that management should attempt to ensure minimal disturbance to environmental variables underlying the spatial variation in macroinvertebrate assemblages. Background enrichment indices showed that the health of Jafari Creek has declined over time due to the constant discharge of heavy metals to the Creek system. These indices also identified a significant degree of pollution in the study area. The decrease in the ecological potential of Jafari Creek was best highlighted by the alteration in macrobenthic assemblages.