Fluorescent cyanine and squaraine dyes are described that can be conjugated to analyte molecules of interest such as peptides, proteins, nucleic acids, RNA, DNA, carbohydrates, polymers and small molecules via a sulfonyl or sulfonamide substituent. The new dyes are made via a novel cyanine dye activation procedure that converts the normally stable, water solubilizing sulfonate substituents into a reactive sulfonyl halides. The sulfonyl halides may be directly conjugated to analytes or can be further converted to more stable reactive sulfonamide handles or to water soluble sulfonamides. The general structure of the new dyes is given below where the central linker is an unsaturated carbon chain or an unsaturated chain containing a squaraine moiety.