The process of metal bioaccumulation in marine food chains is poorly understood because very little data is available on metal concentration at different trophic levels and their temporal or spatial variation. Because of that, we were interested to (1) determine the concentration range of heavy metals in seaweed and seagrasses species in Magdalena Bay; (2) describe the spatial and temporal variation of heavy metal concentrations in the seaweeds and seagrasses. Seasonal collections were done at Estero Banderitas in November 2004, February, and April 2005 wherein we divided the estuary into three major areas (upper, middle, and lower), and within each area, two sites were selected. Our results showed that iron, copper, and magnesium were the most significant metals found in seagrasses, red, and green algae. We found significant more variation in temporal heavy metal concentrations in relation to the maximum abundance in the samples and spatial variation in relation to the studied taxa suggesting that hervibores have a differential intake of the metals. Also, our results suggest that heavy metals might be incorporated regularly in the diet of many herbivorous animals with severe consequences to their health. Management strategies for these species should consider monitoring the levels of metals.