Marine phytoplankton photosynthetic efficiency is regulated by light and nutrient availability, which are both modulated by physical processes in the stratified water column. The ecological impact of such forcings depends on the alignment of biological and physical processes across comparable spatial and temporal scales. During summer stratification in the southern Adriatic Sea, internal island-trapped wave (ITW) induces vertical thermocline oscillations of up to 30 meters. In order to investigate their influence on net primary production, field campaigns were conducted during stratification periods from 2021 to 2023. The aim of this research was to quantify net primary production rates, to relate them to biophysical conditions of the water column and to characterize biophysical coupling within the thermocline. Six <em>in situ</em> <sup>14</sup>C primary production experiments were conducted, while high-resolution datasets on plankton community structure and physico-chemical parameters were obtained. Results revealed a strong biophysical coupling in the thermocline layer driven by the interaction between ITW, plankton communities and broader food web dynamics. The ITWs were associated with increased nutrient concentrations and light availability in the thermocline layer, coinciding with enhanced photosynthetic activity and primary production rates, particularly for pico- and nanophytoplankton. Net primary production was regulated by resource availability, zooplankton grazing and microbial recycling, highlighting the importance of trophic interactions under ITW forcing. This study demonstrates that ITW can modulate net primary production, therefore enhancing productivity in the stratified oligotrophic ecosystems. Such biophysical coupling at small spatio-temporal scale may play a vital role in regulating ecosystem functioning under climate change-driven prolonged stratification.