Eutrophication is a major environmental issue with many negative consequences, such as hypoxia and harmful cyanotoxins production. Monitoring coastal eutrophication is a crucial, especially for island countries like the Republic of Cyprus, which are economically dependent on the touristic sector. Additionally, the open-sea aquaculture industry in Cyprus has been exhibiting an increase in the last decades and environmental monitoring to identify possible signs of eutrophication is mandatory according to the legislation. Therefore, in this modelling study, two different types of Artificial Neural Networks (ANNs) are developed based on in situ-data collected from stations located in the coastal waters of Cyprus. Theses ANNs aim to model the eutrophication phenomenon based on two different data-driven modelling procedures. Firstly, the self-organizing map (SOM) ANN examines several water quality parameters (specifically water temperature, salinity, nitrogen species, ortho-phosphates, dissolved oxygen and electrical conductivity) interactions with the Chlorophyll-a parameter. The SOM model enables us to visualize the monitored parameters relationships and to comprehend complex biological mechanisms related to Chlorophyll-a production. A second feed-forward ANN model is also developed for predicting the Chlorophyll-a levels. Based on this ANN model, several scenarios associated to the eutrophication-related water quality parameters can be extracted. The combination of these two ANNs models is considered a holistic modelling approximation for the identification of eutrophication scenarios, since it enables not only the prediction of the Chlorophyll-a parameter levels, but also the “capturing” of hidden biological mechanisms associated with algal production.