Size structure of phytoplankton determines to a large degree the trophic interactions in oceanic and coastal waters and eventually the destiny of its biomass. Although, tropical estuarine systems are some of the most productive systems worldwide compared to temperate systems, little is known about phytoplankton biomass size fractions, their contribution to net metabolism, or the ecological factors driving phytoplankton size distribution in tropical estuaries. Hence, we measured the size-fractionated biomass and net metabolism of the plankton community along a salinity and nutrient gradient in the Gulf of Nicoya estuary (Costa Rica), during the dry season. Respiration (23.6 mmol O2 m−3 h−1) was highest at the estuary head, whereas maximum net primary production (23.1 mmol O2 m−3 h−1) was observed in the middle of the estuary, coinciding with the chlorophyll a maximum (15.9 mg m−3). Thus, only the middle section of the estuary was net autotrophic (2.9 g C m−2 d−1), with the rest of the estuary being net heterotrophic. Regression analysis identified light availability, and not nutrients, as the principal factor limiting primary production in the estuary due to increased turbidity. The changes in net metabolism along the estuary were also reflected in the phytoplankton's size structure. Although micro- and picophytoplankton were the most productive fractions overall, in the middle section of the estuary nanophytoplankton dominated primary production, chlorophyll, and autotrophic biomass.