Metal concentrations in coastal zones are a critical study subject since anthropogenic activities surrounding these zones are increasing and affecting environmental concentrations of metals. Macroalgae have been used as biomonitors since they can act as indicators of metal concentrations in the water column. Tissue samples of three abundant macroalgae species (Spyridia filamentosa, Padina mexicana and Ulva ohnoi) were collected from three sites with different anthropogenic impacts at La Paz Bay and Guaymas Bay, Mexico, during three contrasting seasons (dry, rainy and cold) in the year 2016. Tissue concentrations of iron (Fe), manganese (Mn), copper (Cu), zinc (Zn), nickel (Ni), cadmium (Cd) and lead (Pb) were determined by atomic absorption spectrophotometry. The highest concentrations were found in S. filamentosa inhabiting both bays. The highest Cd and Mn concentrations were recorded in algae from La Paz Bay, while the highest concentrations of Cu, Zn, Pb and Fe were recorded in algae from Guaymas Bay. Metal concentrations varied seasonally; the highest Fe, Cu, Zn, Ni and Pb levels were recorded in the cold season in algae from both bays. S. filamentosa concentrated more Fe, Ni, Cu, Zn and Pb, while P. mexicana and U. ohnoi showed higher Mn and Cd. Therefore, S. filamentosa proved to be the most suitable indicator of metal concentrations, followed by P. mexicana and U. ohnoi. The high metal concentrations recorded in algae from San Juan de la Costa, La Paz Bay, are related to mining activities, whereas those in algae from Guaymas Bay are related to canneries, maritime traffic and others.