Density, biomass, morphology, phenology and photosynthetic characteristics of Zostera marina were related to continuous measurements of in situ irradiance, attenuation coefficient and temperature at three coastal lagoons in Baja California, Mexico. In situ irradiance was approximately two-fold lower at San Quintin Bay (SQ) than at Ojo de Liebre Lagoon (OL) and San Ignacio Lagoon (SI). As a consequence of the greater irradiance, plants at OL and SI were established 1 m deeper within the water column than those at SQ. At SQ, there was a four-fold variation in biomass of Z. marina caused by changes on shoot length and not shoot density, while at OL and SI biomass and shoot length did not fluctuate significantly throughout the year. Reproductive shoot density reached maximum values concomitantly with the greatest irradiance during spring-summer, however, the density was approximately three-fold greater at SQ than at the southern coastal lagoons. While irradiance levels were two-fold greater at the southern lagoons, in general, photosynthetic characteristics were similar among all three lagoons. The hours of light saturated photosynthesis, calculated from their photosynthetic characteristics and irradiance measurements, suggest that photosynthesis of shoots from OL and SI are saturated for more than 6 h per day throughout the year, while shoots from SQ are likely light limited during approximately 15% of the year. Consequently, an increase in attenuation coefficient values in the water column will likely decrease light availability to Z. marina plants at SQ, potentially decreasing their survival.