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Coastal habitats provide important ecosystem services, such as the maintenance of ecological sustainability, water quality regulation, nutrient recycling, and sandy beaches which are important areas for recreation and tourism. The quality of seawater is generally measured by determining the concentrations of Escherichia coli and intestinal Enterococci, which might be affected by the persistent populations of these bacteria in sand. Sand might thus be a significant source of pathogen exposure to beachgoers. The quality of coastal recreational waters can also be affected by eutrophication, water discoloration, and harmful algal blooms, which pose additional human health risks. Here, we conducted a monitoring of the beaches quality along the Taranto Gulf by determining the concentrations of fecal indicator organisms, as well as other parameters that are not traditionally measured (physicochemical parameters, Pseudomonas aeruginosa, and harmful microalgae), in shallow seawater and sand sampled from three beaches. The concentrations of bacteria were determined using both standard microbiological methods and the IDEXX system. Our results demonstrate the utility of measuring a greater number of parameters in addition to those conventionally measured, as well as the importance of assessing the health risks posed by the sand matrix. Additional work is needed to develop rapid analytical techniques that could be used to monitor the microbiological parameters of solid matrices., (© 2022. The Author(s).)