Coastal zones are important areas for the development of diverse ecosystems. The analysis of chlorophyll a (Chl a), as an indicator of primary production in these regions, is crucial for the quantification of phytoplankton biomass, which is considered the main food chain base in the oceans and an indicator of the trophic state index. This variable is greatly important for the analysis of the oceanographic variability, and it is crucial for determining the tendencies of change in these areas with the objective of determining the effects on the ecosystem and the population dynamics of marine resources. In this study, we analysed the Chl a concentration distribution on the mainland coast of the Gulf of California based on the monthly data from July 2002 to July 2019, obtained from remote sensing (Moderate-Resolution Imaging Spectroradiometer Aqua (MODIS-Aqua) with a 9 km resolution). The results showed a clear distribution pattern of Chl a observed along this area with the maximum levels in March and minimum levels in August. A four-region characterisation on this area was used to make a comparison of the Chl a concentrations during warm and cold periods. The majority of the results were statistically significant. The spectral analysis in each of the four regions analysed in this study determined the following variation frequencies: annual, semi-annual, seasonal, and inter-annual; the last was related to the macroscale climatological phenomena El Niño-La Niña affecting the variability of the Chl a concentration in the study region.