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The short term impacts of fishing pressure were compared with the variability induced by environmental drivers on quantitative benthic community impact indicators. The different pressures were evaluated through comparative multifactor statistical analyses of their effects on macrofauna indicators in a Baltic Sea area with high natural disturbance. The area is exposed to a wide range of fishing intensities from long term non-fished areas to seasonal and annually frequently fished areas. Such evaluations are important for comparing the influence and short term variability of impact indicators from both demersal fisheries and the environment, including benthic community biodiversity (species richness), density (abundance in number of individuals), biomass, and average individual mean weight, with high spatio-temporal resolution. Environmental drivers include near bottom water current speed, salinity, temperature, and dissolved oxygen concentration, considering habitat specific and seasonal conditions. Demersal fishing-induced impacts were evident for all indicators. The highest fishing impacts were estimated in soft muddy and sandy habitats and in the second quarter of the year for all indicators, considering complex interactions. All environmental drivers, especially, current speed, had significant impacts on all indicators. The significant influences and short term variability caused by environmental drivers were of the same or larger order of magnitude as fishing impacts. Consequently, the short term influence of environmental drivers and seasonal differences in fishing pressure need to be considered when using quantitative benthic fishing impact indicators and identifying areas that are more or less resilient to fishing in relation to short- and long-term fisheries management plans.