The influence of benthic suspension feeders as bioremediating organisms on water column seston and their ability to mitigate fish farm waste was assessed by monthly analyses for one year. A monthly monitoring from July 2020 to October 2021 of physico-chemical and biochemical variables of the water column and the sediment was performed in an in-shore mariculture plant located in the Mar Grande of Taranto (Italy), comparing two adjacent areas that differ in type of farming. The first (reference site) is a fish monoculture, while the second consists of an innovative Integrated Multi-Trophic Aquaculture system (IMTA site). The annual cycle of chlorophyll-a concentration showed values corresponding to mesotrophic/eutrophic conditions, with peak production in early fall (4.64 μg L−1). During the spring and summer sampling times, when the amount of aquaculture waste is greater than during the rest of the year, the reference site showed the highest lipid (151.73 μg L−1) and organic matter (189.00 mg g−1) values with respect to those at the IMTA site. The IMTA bioremediating organisms possibly acted as underwater gardens changing the seston quality and availability and providing protection and food for the zooplankton community, which showed higher abundance of individuals for most sampling times at the IMTA site, peaking during September and October in both 2020 and 2021 (max 232,985.20 ind m−3). Our results demonstrate the effectiveness of the considered IMTA system in mitigating the negative impact of organic matter release into the environment due to fish farming activities. The influence of bioremediating organisms on seston composition and concentration opened up mitigation as well as restoration scenarios.