HIDRALERTA is a forecast and early warning system for coastal and port regions capable of predicting emergency situations, as well as carrying out risk assessment. The system concentrates on evaluating wave overtopping and flooding scenarios. It uses offshore sea-wave and wind forecast data, as well as tide data, as input to determine wave overtopping at specific locations. The calculation of the mean overtopping discharge over a structure is made through artificial neural network tools and/or empirical formulae, which are able to define the spatial distribution of the flow behind the structure. The HIDRALERTA system is composed of four modules developed in Open Source Web Technology, mainly using the Python Language. The Warning System can be configured and adapted for specific scenarios. The system has been successfully tested for the Port and Bay of Praia da Vitória, Terceira Island, Azores, Portugal, and is now under development and being implemented at the ports of Madalena do Pico and S. Roque do Pico. This paper describes the work carried out to date on the system and its application to these two ports in the Pico Island, Azores.