BODIPY-hydroporphyrin energy transfer arrays allow for development of family of fluorophores featuring a common excitation band at 500 nm, tunable excitation band in deep red/near-infrared window, and tunable emission. Their biomedical applications are contingent upon retaining their optical properties in aqueous environment. Amphiphilic arrays containing PEG-substituted BODIPY and chlorins or bacteriochlorins were prepared and their optical and fluorescence properties were determined in organic solvents and aqueous surfactants. The first series of arrays contains BODIPYs with PEG substituents attached to the boron, whereas in the second series, PEG substituents are attached to the aryl at the meso positions of BODIPY. For both series of arrays, excitation of BODIPY at 500 nm results in an efficient energy transfer to and bright emission of hydroporphyrin in deep-red (640–660 nm) or near-infrared (740–760 nm) spectral windows. In aqueous non-ionic surfactants (Triton X-100 and Tween 20) arrays from the second series exhibit significant quenching of fluorescence, whereas properties of arrays from the first series are comparable to those observed in polar organic solvents. Reported arrays possess large effective Stokes shift (115 – 260 nm), multiple excitation wavelengths, and narrow, tunable deep-red/near-IR fluorescence in aqueous surfactants, and are promising candidates for a variety of biomedical-related applications.