Microalgae have emerged as a promising feedstock for the sustainable production of lipid-based products, including biofuels and omega-3 fatty acids, by utilizing CO2 as a carbon source. Glycerol-3-phosphate dehydrogenase (GPDH) is a vital enzyme in microalgal lipid synthesis, converting dihydroxyacetone phosphate into glycerol-3-phosphate, the initial substrate for the Kennedy pathway responsible for triacylglycerol production. In this study, we identified and overexpressed a chloroplastic NAD(P)(+)-dependent GPDH (NsGPDH1) in Nannochloropsis salina. Quantitative reverse transcription polymerase chain reaction and western blotting revealed increased NsGPDH1 expression in the transformants as compared to wild-type N. salina. This overexpression of NsGPDH1 resulted in increased glycerol production and a higher proportion of mono-unsaturated fatty acids, which are indicative of GPDH overexpression. Notably, lipid productivity in NsGPDH1-overexpressing N. salina strains increased by 40% without significant growth defects. These results highlight the effectiveness of NsGPDH1 overexpression as a strategy for enhancing lipid biosynthesis in N. salina, contributing to the advancement of microalgae-based lipid production.