Two new 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) dyes (1 and 2) with piperazine subunits on position 3 or 5 were synthesized. Their absorption and steady-state fluorescence properties were investigated as a function of solvent. In water/MeCN (9:1, V/V) solution, the dyes show fluorescent enhancement upon increasing the acidity of the solution. They can be used in water/MeCN (9:1, V/V) solution as fluorescent pH probes excitable with visible light, with pKa values near-neutral (around 6.5 and 6.8). Dyes 1 and 2 are readily taken up by biological cells in the cytosol where it has no obvious toxic effects.