Fluorescent silica nanoparticles (NPs-(SiO2-Fluo)) were synthesized based on the classical Storber method for cyanobacteria labelling. Modified mono-coloured SiO2 NPs with fluorescein (Fl) and rhodamine B (RhB)were obtained (NPs-(SiO2-Fl) and NPs-(SiO2-RhB)). Moreover, multi-coloured SiO2 NPs, via the incorporation of both emitters (NPs-(SiO2-RhB-Fl)), were tuned for optimal emissions and the biodetection of cyanobacteria. NPs-(SiO2-Fl) and NPs-(SiO2-RhB-Fl) were optimized for detection via laser fluorescence microscopy and in-flow cytometry with laser excitation and fluorescence detection. By TEM, homogeneous SiO2 NPs of 180.0 nm in diameter were recorded. These sizes were slightly increased due to the covalent linking incorporation of flu...