Variability of the optical properties of the northern Gulf of California (México) were analyzed for the first time based on six cruises performed from spring to summer (March to September) between 2008 and 2013. The changes observed in the absorption by three seawater components (phytoplankton, detritus and chromophoric dissolved organic matter or CDOM) were analyzed in relation to changes in bio-optical regions and composition of the phytoplankton community (determined based on phytoplankton pigments). Two regions with unique bio-optical characteristics were identified separated by a narrow transition zone: the Upper Gulf of California (UGC) and Northern Gulf of California (NGC). Despite the temporal changes in their spatial distribution they maintained particular characteristic. UGC is characterized by an average Chla of 1.78 mg/m3, the dominance of microphytoplankton (diatoms and dinoflagellates) and a stronger contribution of detritus to total light absorption. NGC is characterized by an average Chla of 0.7 mg/m3 and the predominance of picophytoplankton, characterized by the dominance of zeaxanthin (marker pigment for cyanobacteria) and/or chlorophyll b (marker pigment for green algae), along with a co-dominium by CDOM and phytoplankton to light absorption. Results indicate that Case II waters can be very different when evaluating the individual contribution by phytoplankton, detritus and CDOM to total light absorption what has to be considered for the selection of bio-optical models for each specific region what can also help to a better definition of the related uncertainties.