Eutrophication is a major environmental issue with many negative consequences, such as hypoxia and harmful cyanotoxin production. Monitoring coastal eutrophication is crucial, especially for island countries like the Republic of Cyprus, which are economically dependent on the tourist sector. Additionally, the open-sea aquaculture industry in Cyprus has been exhibiting an increase in recent decades and environmental monitoring to identify possible signs of eutrophication is mandatory according to the legislation. Therefore, in this modeling 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. These ANNs aim to model the eutrophication phenomenon based on two different data-driven modeling 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 (Chl-a) parameter. The SOM model enables us to visualize the monitored parameters’ relationships and to comprehend complex biological mechanisms related to Chl-a production. A second feed-forward ANN model is also developed for predicting the Chl-a levels. The feed-forward ANN managed to predict the Chl-a levels with great accuracy (MAE = 0.0124; R = 0.97). The sensitivity analysis results revealed that salinity and water temperature are the most influential parameters on Chl-a production. Moreover, the sensitivity analysis results of the feed-forward ANN captured the winter upwelling phenomenon that is observed in Cypriot coastal waters. Regarding the SOM results, the clustering verified the oligotrophic nature of Cypriot coastal waters and the good water quality status (only 1.4% of the data samples were classified as not good). The created ANNs allowed us to comprehend the mechanisms related to eutrophication regarding the coastal waters of Cyprus and can act as useful management tools regarding eutrophication control.