We compared the common methods of chlorophyll measurement in Lemna minor (duckweed), Potamogeton crispus, and Egeria densa in an attempt to identify an optimal protocol to quickly measure chlorophyll in aquatic plants. Three physical processes including grinding-settling (GS), grinding-elution (GE) and immersing (IM) were compared for chlorophyll extraction in 80% acetone with duckweed. Then, the GE method was chosen for tissue rupture, and the efficiency of three solvents (80% aqueous acetone, 90% aqueous acetone and 95% aqueous ethanol) on chlorophyll extraction was tested on duckweed, P. crispus, and E. densa. There was no difference in the amount of chlorophyll extracted between the procedures of GE and GS, or between GE and IM. The amount of total chlorophyll extracted by 90% acetone was higher than that extracted by 80% acetone or 95% ethanol in the three aquatic plants. Furthermore, the chlorophyll extracted by and held in 90% acetone was more stable over time than it was with either 80% acetone or 95% ethanol. Therefore, the procedure of grinding-elution for physical rupture and 90% acetone for extraction is recommended as a quick and reliable protocol for chlorophyll extraction in aquatic plants.