Adverse effects of wastewater treatment plants (WWTPs) on sediment quality at the Bay of Cádiz (SW, Spain) were evaluated by a battery of acute bioassays and chemical contamination. Five sites directly affected by WWTPs effluents and one control site were chosen. Results evidenced clear deterioration of ecological sediment quality parameters and possible effects on aquatic communities towards WWTPs areas. Acute toxicity and chemical contamination varied significantly across the studied sites and differed between winter and summer seasons. The Bay of Cádiz is contaminated by PAHs, metals, detergents (SAS) and pharmaceutical products. Principal Component Analyses indicated metals, SAS and pharmaceutical products as the major environmental stresses. Sea-urchin embryo-larval and microalgae growth rate were the most sensitive bioassays to evaluate resuspension of contaminants (elutriate) from bulk sediment. Amphipods mortality and Microtox(®) solid phase test bioassays were recommended to evaluate bulk sediment quality. Therefore, the use of multiple-bioassays, sensitive to sediment pollution, may provide complementary information to diagnose environmental factors that can impair aquatic communities. The battery of bioassays is recommended to assess and monitor marine sediments directly affected by a mixture of contaminants released from WWTPs.