This study seeks to elucidate the spatial and temporal patterns of toxic phytoplankton in coastal waters of the Balearic Archipelago (NW Mediterranean Sea) in a multivariate approach. We also examine whether there is a direct relationship between the abundance of toxic phytoplankton and the physical-chemical parameters and different human pressure activities. Its magnitude and the species-specific pattern are also evaluated. The study is based on chlorophyll a and phytoplankton composition and abundance, as well as physical and chemical data, to evaluate the ecological status of Balearic waters for the implementation of the Water Framework Directive. A total of 24 taxa included in the Intergovernmental Oceanographic Commission toxic algae checklist and five well-known bloom formers were identified. Principal Component Analysis (PCA) for physical-chemical and human uses revealed the larger phytoplankton variability determined by seasonal patterns. Higher nutrient winter samples were distinguished from those of high transparency and lower nutrient summer waters. The Redundancy Analysis (RDA) separated the toxic species into two groups: Pseudo-nitzschia species, related to winter; and dinoflagellates and other flagellates species, related to spring and summer. The among-islands effect revealed a latitudinal gradient, especially regarding nutrient and human pressures related to Mallorca Island. Meanwhile, the Formentera waters were transparent and far from human activities.