A systematic sampling programme war carried out in a large number of confined waters (principally harbours) along the Catalan coast (NW Mediterranean) in the context of a new Monitoring Programme. This Monitoring Programme was associated not only with areas subject to aquaculture activities, and therefore under legislation, but also with confined areas with a high risk of harmful algal blooms (HABs) occurrence, in order to provide an early warning of potentially widespread HABs. The systematic Programme war Performed weekly in summer and bi-monthly in winter for five-years. The main results were: (i) the detection of many harmful species and the presence of high numbers of harmful dinoflagellates, mainly of the genera Alexandrium and Dinophysis; (ii) the detection of Alexandrium catenella, new in the study area, which had hardly ever been detected in the Mediterranean Sea; (iii) the presence of some potentially harmful species, including Dinophysis sac culus, present at all periods of the year; (iv) bloom recurrence in several stations; (v) occasional coincidence of small-scale blooms, such as those confined inside the harbours, with widespread blooms (mesoscale blooms) of the same organism. The implications of this high frequency of HAB detection is discussed in relation to the suitability of this sampling programme (focused on confined waters) for the early detection of algal blooms.