An evaluation of the vertical distribution of chlorophyll-a (Chl-a) levels, as an indicator of phytoplankton biomass, has strong repercussions in any marine ecosystem since it allows evaluating its productive potential and the amount of matter that is available for the higher trophic levels of the pelagic food web. This short communication aims to report the vertical distribution patterns of Chl-a levels and some selected hydrographic parameters during autumn in the Bay of La Paz, the biggest and deepest coastal environment inside the Gulf of California, a site also recognized for its high biodiversity. Two oceanographic research cruises were carried out during November 2014 and 2016. A CTD probe configured with dissolved oxygen and active fluorescence sensors, all pre-calibrated by the manufacturer, was used to acquire high-resolution data along the water column. The results showed two distribution patterns of Chl-a: 1) deep peaks (>60 m depth, with concentrations >6 mg m-3) associated with the bottom at nearshore stations, and 2) maximum concentration peaks associated with the thermocline/pycnocline with concentrations up to 7.40 mg m-3 observed at deep stations. A multivariate statistical analysis confirmed the role played by some physical variables in the distribution patterns described. The results shown in this study complement the previous research and fill in the existing gaps for the transition periods between the warm and the cold.