Relationships among chemical–physical features, total gross suspended organic matter, coverage of the seagrass Ruppia cirrhosa and its associated algal community in eight ponds of a saltworks system of western Sicily (Mediterranean Sea) were investigated in spring and summer 2004. All biological features varied both at different levels of seagrass coverage and between seasons. A low algal diversity (46 taxa, 14.75 ± 1.41 on average) was highlighted; algal coverage and species richness showed to be negatively correlated. Ruppia cirrhosa coverage was negatively correlated with algal coverage, but positively correlated with species richness. Moreover, a significant correlation among R. cirrhosa coverage, the availability of suspended matter in the water column and the chlorophyll a concentration was detected.