Shellfish sanitary controls are very important to guarantee consumer health because bivalve molluscs (BVM) are filter-feeders so they can accumulate pathogens, environmental contaminants and biotoxins produced by some algae, causing infections and food poisoning in humans after ingestion. The purpose of this work was to analyse with chemometric methods the historical data relating to routine analyses carried out by the competent authority (Liguria Local Health Unit, National Health Service) on the BVM reared in a shellfish farm located in the Gulf of La Spezia (Italy). Chemometric analysis was aimed at identifying any correlations between the variables, as well as any seasonal trends and similarities between the stations, in order to be able to provide further material for a more accurate risk assessment and to improve the monitoring organization for example by reducing sampling stations and/or sampling frequency. The dataset used included 31 variables classified as biotoxicological, microbiological and chemical variables, measured twice a week, monthly or half yearly respectively, for a total of 6 years (from 2015 to 2021), on samples ofMytilus galloprovincialiscoming from 7 monitoring stations. The results obtained by the application of principal component analysis have shown positive alga-biotoxin correlations, as well as seasonal trends linked to algae growth, with a greater algal biomass and their toxins during the spring months. In addition, periods characterised by low rainfall were found to affect algal development, promoting especially species such asDinophysisspp. Considering the microbiological and biotoxicological variables, significant differences between the monitoring stations were not found. However, stations could be distinguished on the basis of the nature of the predominant chemical pollutants.