Saltworks are interesting sites for aquatic ecology, where marine phytoplankton plays a fundamental role in regulating ecosystem processes and sustaining large-scale biodiversity. This paper presents successional, structural, and dynamical traits of a phytoplankton metacommunity in a disused saltwork, where the industrial hydraulic management has been changed, leading to a different overlapping of natural and anthropic induced scales. We have considered the total phytoplankton biomass, size classes, and chemotaxonomical composition in monitoring the metacommunity dynamics in a series of single ponds spanning from marine to hypersaline ones between July 2008 and October 2009. Results indicate a large accumulation of biomass during summer to early autumn in hypersaline ponds, with the prevalence of small-size cells (<20 μm) in the entire system. Despite severe salinity fluctuations as a consequence of rainy events and evaporating processes, chlorophytes represented the dominant group of hypersaline ponds, while diatoms were more abundant where the influence of seawater inflow was higher. Despite the absence of ordinary maintenance, the phytoplankton metacommunity dynamic and patterns observed suggest that the existing saline gradient ensures qualitative and quantitative aspects of the primary production usually found in active saltworks. This makes the Saline di Tarquinia an important site not only for the preservation of Mediterranean biodiversity and hypersaline biotopes but also for ecological studies dealing with the trait-based responses of the phytoplankton community to large environmental fluctuations.