Polyphosphate, a linear polymer of orthophosphate, is abundant in the environment and a key component in wastewater treatment and many bioremediation processes. Despite the broad relevance of polyphosphate, current methods to quantify it possess significant disadvantages. Here, we describe a new approach for the direct quantification of inorganic polyphosphate in complex natural samples. The protocol relies on the interaction between the fluorochrome 4',6-diamidino-2-phenylindole (DAPI) and dissolved polyphosphate. With the DAPI-based approach we describe, polyphosphate can be quantified at concentrations ranging from 0.5-3 microM P in a neutral-buffered freshwater matrix with an accuracy of +/-0.03 microM P. The patterns of polyphosphate concentration versus fluorescence yielded by standards exhibit no chain length dependence across polyphosphates ranging from 15-130 phosphorus units in size. Shorter length polyphosphate molecules (e.g., polyphosphate of three and five phosphorus units in length) contribute little to no signal in this approach, as these molecules react only slightly or not at all with DAPI in the concentration range tested. The presence of salt suppresses fluorescence from intermediate polyphosphate chain lengths (e.g., 15 phosphorus units) at polyphosphate concentrations ranging from 0.5-3 microM P. For longer chain lengths (e.g., 45-130 phosphorus units), this salt interference is not evident at conductivities up to approximately 10mS/cm. Our results indicate that standard polyphosphates should be stored frozen for no longer than 10-15 days to avoid inconsistent results associated with standard degradation. We have applied the fluorometric protocol to the analysis of five well-characterized natural samples to demonstrate the use of the method.