In most plants and algae, a down-regulation of photosynthesis under "excess" light conditions occurs which is associated with a quenching of chlorophyll a fluorescence. This nonphotochemical quenching of chlorophyll a fluorescence most likely arises from a mechanism which protects photosystem II from excessive excitation and resulting photoinhibition. In this report, nonphotochemical quenching of variable chlorophyll a fluorescence was induced by low pH in photosystem II enriched spinach thylakoid membranes. The origin of quenching was investigated with picosecond fluorescence decay spectroscopy in samples suspended in buffers ranging from pH 6.5 to pH 4.0. The yield of a relatively slow (approximately 1.5 ns) fluorescence decay process associated with the photosystem II reaction center decreased with decreasing pH. There were no significant changes in the yield of faster decay components associated with photosystem II antenna chlorophyll a processes. These results suggest a reaction center based rather than antenna chlorophyll based mechanism for nonphotochemical quenching in these preparations. Measurements of the photosystem II absorption cross section revealed no decrease in the functional antenna size at low pH which also supports a reaction center quenching mechanism. The kinetics of electron transfer in photosystem II were investigated using a pump probe spectrometer which measured simultaneously the flash-induced absorbance change at 820 nm (formation of oxidized photosystem II reaction center pigment, P680+) and the variable fluorescence yield (formation of reduced photosystem II, electron acceptor, QA-). A large increase in the lifetime of P680+ at low pH was correlated with fluorescence quenching. After flash excitation of photosystem II the loss of fluorescence quenching occurred with the same kinetics as the reduction of P680+. In conflict with reaction center based quenching mechanisms based on charge recombination between P680+ and QA-, the oxidation rate of QA- was unaffected by low pH and under all conditions occurred at a slower rate than the reduction of P680+. Our data are discussed in terms of a model for low pH dependent nonphotochemical quenching in photosystem II based on direct quenching by P680+.