This invention relates to water-soluble mono-alkoxy and mono-alkyne BODIPY derivatives, including methods for making the same. For examples, provided herein are compounds of Formula (I): or a pharmaceutically acceptable salt thereof, wherein: is a BODIPY ligand system; X is a halogen; L is absent or a linker; and Z is selected from the group consisting of: a group reactive with a biologically active molecule and a detectable agent.