The study of biotic and abiotic factors and their interrelationships is essential in the preservation of sustainable marine ecosystems and for understanding the impact that climate change can have on different species. For instance, phytoplankton are extremely vulnerable to environmental changes and thus studying the factors involved is important for the species’ conservation. This work examines the relationship between phytoplankton and environmental parameters of the eastern equatorial Pacific, known as one of the most biologically rich regions in the world. For this purpose, a new multivariate method called MixSTATICO has been developed, allowing mixed-type data structured in two different groups (environment and species) to be related and measured on a space–time scale. The results obtained show how seasons have an impact on species–environment relations, with the most significant association occurring in November and the weakest during the month of May (change of season). The species Lauderia borealis, Chaetoceros didymus and Gyrodinium sp. were not observed in the coastal profiles during the dry season at most stations, while during the rainy season, the species Dactyliosolen antarcticus, Proboscia alata and Skeletonema costatum were not detected. Using MixSTATICO, species vulnerable to specific geographical locations and environmental variations were identified, making it possible to establish biological indicators for this region.