Arctic fjords are hotspots of marine carbon burial, with diatoms playing an essential role in the biological carbon pump. Under the background of global warming, the proportion of diatoms in total phytoplankton communities has been declining in many high-latitude fjords due to increased turbidity and oligotrophication resulting from glacier melting. However, due to the habitat heterogeneity among Svalbard fjords, diatom responses to glacier melting are also expected to be complex, which will further lead to changes in the biological carbon pumping and carbon sequestration. To address the complexity, three short sediment cores were collected from three contrasting fjords in Svalbard (Krossfjorden, Kongsfjorden, Gronfjorden), recording the history of fjord changes in recent decades during significant glacier melting. The amino acid molecular indicators in cores K4 and KF1 suggested similar organic matter degradation states between these two sites. In contrast to the turbid Kongsfjorden and Gronfjorden, preserved fucoxanthin in Krossfjorden indicated a continuous increase in diatoms since the mid-1980s, corresponding to a 59 % increase in biological carbon pumping, as quantified by the δ13C of sedimentary organic carbon. The increasing biological carbon pumping in Krossfjorden is further attributed to its hard rock types in the glacier basin, compared to Kongsfjorden and Gronfjorden, which are instead covered by soft rocks, as confirmed by a one-dimensional model. Given the distribution of rock types among basins in Svalbard, we extrapolate our findings and propose that approximately one-fifth of Svalbard's fjords, especially those with hard rock basins and persistent marine-terminated glaciers, still have the potential for an increase in diatom fractions and efficient biological carbon pumping. Our findings reveal the complexity of fjord phytoplankton responses and biological carbon pumping to increasing glacier melting, and underscore the necessity of modifying Arctic marine carbon feedback to climate change based on results from fjords underlain by hard rocks.