This study evaluates the influence of man-made activities on the benthic environment at two different marinas: Southsea Marina on the south coast of England, and Minimes Marina on the Atlantic coast of France. We assessed the differences in: (1) sediment percentage organic matter, particle size and heavy metal concentration, using copper (Cu), cadmium (Cd), zinc (Zn) and lead (Pb) as contamination indicators; (2) sediment elutriate toxicity (LC50) using algal (Fucus serratus) bioassay; and (3) benthic community characteristics (number of species, abundance, most contributing species (SIMPER) and biotic index (AMBI)). Canonical correspondence analysis (CCA) was performed to relate the abundance of species to the environmental variables. At both marinas, we observed an increasing gradient of contamination from outside to the innermost sites. At both marinas, the lowest macrofaunal abundance was recorded at the innermost sites and differences in benthic community structure were observed between sites. At Southsea Marina, the cirratulids Tharyx marioni and T. killariensis and the cossurid Cossura pygodactylata dominated sites outside, while the opportunistic species Capitellides girardi dominated the innermost sites. At Minimes Marina, the cirratulid Streblospio shrubsolii was abundant outside and at the middle sites but was almost absent at the innermost sites. The biotic index—AMBI—indicated that sediments in the innermost sites were heavily disturbed at Southsea Marina and slightly to moderately disturbed at Minimes Marina. In Southsea, the AMBI was positively correlated to the sediment metal concentrations (Cu, Zn and Cd) and elutriate toxicity (LC50), while in Minimes the AMBI was positively correlated to the % of sediment fine particle and elutriate toxicity (LC50).