Monitoring the impact of the pollutants on the sea is a crucial issue for coastal human activities, such as aquaculture. However, leveraging a continuous microbiological laboratory analysis is unfeasible for costs and practical reasons. Fish and mussel farms are critically sensitive to seawater quality and thus require continuous monitoring to enforce food security and prevent any possible disease affecting human health. Here we present a novel methodology finalized to predict water quality as categorized indexes leveraging an integrated approach between computational components and artificial intelligence techniques. As a paradigm demonstrator, we couple WaComM++ with AIQUAM. The use case presented is an application of AIQUAM in the Bay of Naples (Campania Region, Italy) for predicting bacteria contaminants in mussel farms. The results are encouraging as the model reached a correct prediction rate of 93%.