Cobscook Bay is a shallow, biologically rich, geographically complex, macrotidal estuary located in eastern-most Maine. Seasonal measurements of light attenuation and microalgal biomass as water column phytoplankton and subtidal microphytobenthos were used to estimate primary production using a light and chlorophyll model. The Bay was found to be a high nutrient/low chlorophyll estuary characterized by intense tidal mixing. Seasonal patterns of biomass and productivity indicated a single peak in mid- to late summer that resulted from the growth limiting effects of water column temperature in spring and light availability in fall. Spatial patterns indicated elevated standing stocks in areas where the residence time of waters in the Inner Bay increased, allowing growth to exceed export due to tidal flushing. Site to site comparisons of average water column phytoplankton and subtidal microphytobenthic production demonstrated that suspended microalgae account for only one-tenth of the microalgal productivity of Cobscook Bay since attached microalgae can avoid advective processes and adapt to changes in light availability at short time scales. This example of a high nutrient/low chlorophyll estuary is used to reevaluate the concept of “new” production since nitrate is never limiting and ammonium is present at high concentrations throughout the year.