This data set includes biomass values of phytobenthic species, mainly seaweeds, recorded in the Mar Piccolo of Taranto in the years 2011-2019. Seasonal collection campaigns have been carried out in four stations and three replicates were collected for each station. Starting from 2016 a fifth station was analyzed (40°30'03.15"N; 17°18'30.99"E). For Station 1-4 location see (Petrocelli A., Cecere E., Rubino F. 2019. Successions of phytobenthos species in a Mediterranean transitional water system: the importance of long term observations. Nature Conservation 34: 217-246).