In-situ functionalization of gold nanoparticles with fluorophore-tagged oligonucleotides is studied by comparing femtosecond laser ablation in stationary liquid and in biomolecule flow. Femtosecond laser pulses induce significant degradation to sensitive biomolecules when ablating gold in a stationary solution of oligonucleotides. Contrary, in-situ conjugation of nanoparticles in biomolecule flow considerably reduces the degree of degradation studied by gel electrophoresis and UV-Vis spectrometry. Ablating gold with 100 mu J femtosecond laser pulses DNA sequence does not degrade, while the degree of fluorophore tag degradation was 84% in stationary solution compared to 5% for 1 mL/min liquid flow. It is concluded that femtosecond laser-induced degradation of biomolecules is triggered by absorption of nanoparticle conjugates suspended in the colloid and not by ablation of the target. Quenching of nanoparticle size appears from 0.5 mu M biomolecule concentration for 0.3 mu g/s nanoparticle productivity indicating the successful surface functionalization. Finally, increasing the liquid flow rate from stationary to 450 mL/min enhances nanoparticle productivity from 0.2 mu g/s to 1.5 mu g/s, as increasing liquid flow allows removal of light absorbing nanoparticles from the ablation zone, avoiding attenuation of subsequent laser photons.