Marine biodiversity consists of a complex network of organisms responsible for keeping the ecosystem's balance. Fungi are an understudied group of organisms despite their recognized importance for ecosystem processes and diversity. How fungi respond to environmental change remains poorly understood, especially in marine benthic habitats. The Baltic Sea is a brackish coastal ecosystem with steep environmental gradients in a relatively limited geographical area and is therefore a particularly good system to investigate the impact of different abiotic factors on benthic fungal diversity. This study used environmental DNA (eDNA) metabarcoding to analyze the spatial dynamics of benthic fungal diversity in the Baltic Sea and quantify the environmental drivers that shape these dynamics. Based on 59 stations spreading over 1145 km the results showed that benthic fungal communities were dominated by the phylum Chytridiomycota, and the fungal species Alphamyces chaetifer and Operculomyces laminatus from this phylum were the main drivers of the community structure dissimilarities observed between regions. Water depth and salinity were the main predictors of the benthic fungal community composition. The impact of nutrient availability was also significant, possibly related to the known role of Chytridiomycota species such as A. chaetifer and O. laminatus in nutrient cycling. Our results indicate that the benthic fungal diversity of the Baltic Sea is shaped by salinity gradients and nutrient availability and highlights that the current fungal biodiversity is at risk of species shift or decline with predicted changes in salinity due to climate change and intensified eutrophication.