High-throughput instruments that accurately determine nanoparticle concentration in mixtures, natural waters, and complex media are needed for testing environmental samples and industrial waste streams. Photothermal (PT) microscopy is an optical pump-probe technique that is well suited to address this measurement problem. Unlike commonly used techniques such as coulter counters, single particle mass spectrometry, and nanoparticle tracking analysis, PT can detect very small nanoparticles- observation of stationary 1.4 nm Au has been demonstrated. Impure and complex samples remain a distinct challenge that often requires filtration, which introduces sample loss. Since PT depends on absorption, target particles can be discriminated from a field of scatterers by careful selection of the pump wavelength. Much of the published work involving PT microscopy has focused on stationary, temporally stable samples such as CNTs in tomato plants. However, precedent for detection of diffusing or flowing nanoparticles in aqueous samples was set during the last couple of decades. In addition, advances in technology during the intervening years have opened up paths to quicker, more sensitive PT measurements. In the current program, we have achieved single nanoparticle counting under flow conditions in a microfluidic setup. We are continuing to optimize this technique: in particular, flow rates must be balanced with particle size, concentration, sampling rates, amplifier time constant, and bandwidth settings. When this PT setup is optimized, measurements of nanoparticle concentrations between 109-1011 particles/mL (~10 pM-1 nM) of 5-200 nm Ag and Au particles in complex media may be achieved within minutes. In this talk, the current state of the program, along with challenges and advances will be discussed.