Over the past few decades, harmful algal blooms (HABs) have become increasingly frequent in the fjords and channels of southern Chile. However, knowledge of the environmental factors that trigger them remains limited in remote areas. This study uses a combination of in situ observations and satellite remote sensing (Sentinel-3A/B) to analyse the physical, chemical and biological conditions during a phytoplankton bloom in spring (November–December 2021) in the Magellan region. Fourteen stations were sampled during the EXOFAN cruise to evaluate the hydrographic structure, nutrient availability and phytoplankton composition, paying particular attention to potentially harmful species such as Phaeocystis spp. and the Pseudonitzschia cf. pseudodelicatissima complex. The results revealed spatial heterogeneity in the distributions of salinity, temperature and nutrients, with freshwater inputs and solar heating generating stratified water masses in interior fjords. High cell densities of the target taxa were found in these stable environments, which may act as retention zones favouring bloom persistence. Satellite-derived Sea surface temperature and chlorophyll-a data corroborated the in-situ findings, revealing seasonal warming and productivity hotspots despite frequent cloud cover. This study highlights the importance of combining traditional oceanographic methods with remote sensing to understand and monitor bloom dynamics in complex subpolar coastal systems. The observed patterns offer valuable insights into the ecological conditions that drive HAB development. This information is crucial for the development of future prediction models, early warning systems and sustainable aquaculture management strategies, particularly in the face of ongoing climate-driven changes.