The present study was designed to estimate the critical light intensity required for growth of Zostera marina and that which determines its depth limit. Seeds of Z. marina collected at Matsunase, Ise Bay, Mie Prefecture, central Japan were germinated and grown to young plants of 10 cm in length. The young Z. marina were cultured for 1 week in various water temperatures, and their photosynthesis and respiration were measured under various photon irradiances. The daily compensation point was estimated by a mathematical model based on photosynthetic activity and diurnal changes in solar irradiance. The estimated daily compensation point of young Z. marina was 5.7% of sea surface. The depth limit was determined by the Beer–Lambert law concerning the relative solar irradiance on the sea surface and the extinction coefficient. Almost all previous studies report a shallower growing depth of Z. marina than the present result, but the lowest reported data agreed well with the current estimated depth limit. Therefore, the mathematical model in the present study can estimate the production and critical growing depth of Z. marina. The results suggest that the compensation depth is controlled mainly by the solar irradiance reaching the Z. marina beds.