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A microscale ecological study using the closure approach to understand the impact of productivity controlled by geographical and seasonal variations on the intermittency of phytoplankton is done in this paper. Using this approach for a nutrient–phytoplankton model with Holling type III functional response, it has been shown how the dynamics of the system can be affected by the environmental fluctuations triggered by the impact of light, temperature, and salinity, which fluctuate with regional and seasonal variations. Reynold's averaging method in space, which results in expressing the original components in terms of its mean (average value) and perturbation (fluctuation) has been used to determine the impact of growth fluctuation in phytoplankton distribution and in the intermittency of phytoplankton spreading (variance). Parameters are estimated from the nature of productivity and spread of phytoplankton density during field observation done at four different locations of Tokyo Bay. The model validation shows that our results are in good agreement with the field observation and succeeded in explaining the intermittent phytoplankton distribution at different locations of Tokyo Bay, Japan, and its neighboring coastal regions. [ABSTRACT FROM AUTHOR]