Marine coastal areas have high social-economic relevance and ensuring the good quality of these areas has gained importance in the past decades due to the increase of anthropogenic pressures. Understanding the dynamics of these areas is crucial to support management decisions. In this context, phytoplankton communities are generally used as key indicators of environmental quality as they respond in short time-scales and are at the base of food webs. This work intends to improve our understanding on how phytoplankton communities respond to environmental conditions, particularly in upwelling areas. Seawater samples were collected from Algarrobo Bay, Central Chile, for both phytoplankton pigments and microscopy analysis. Data were analyzed in combination with physico-chemical parameters and two distinct hydrographic regions were identified for the study area: i) a region occupying most of the northern bay section, characterized by lower temperatures and dissolved oxygen (DO), higher concentration of nutrients and higher N:P, where a mixed community with diatoms, chrysophytes, cryptophytes, haptophytes and other small flagellates were observed; and ii) a central-southern section, with higher temperatures and DO, lower nutrients and lower N:P, where diatoms, in particular the centric diatom Chaetoceros Ehrenberg, 1844 sp. (similar to 92.5% on average), dominated the phytoplankton assemblage. Other common but much less abundant diatom genus included Skeletonema Greville, 1865, Eucampia Ehrenberg, 1839, Dactyliosolen Castracane, 1886, Nitzschia Hassall, 1845, Cylindrotheca Rabenhorst, 1859 and Asterionellopsis Round, 1990. Apart from diatoms, the most abundant taxa belonged to flagellates, mainly chrysophytes (228.4 x 10(3) cells L-1 on average) and cryptophytes (213 x 10(3) cells L-1 on average). Overall, results suggest that the southern part of the Algarmbo Bay, with higher residence times and nutrient discharges, may act as an upwelling shadow area, where phytoplankton species can accumulate.