Based on in situ data in Chao Lake from October 15th 2009 to October 16th 2009, two algorithms named Gons and Simis were used to estimate phytoplankton pigment (Chlorophyll-a, Chla; Phycocyanin, PC). Results showed that both Gons and Simis algorithms can be used in waters with algae, but not in waters while algal blooms formed. For the pigment absorption at 665 nm (aph(665)), Gons can provide a better result than Simis. Simis algorithm can be used to estimate PC, while related parameters were re-calibrated. Therefore, it is necessary and significant to validate and develop the algorithms to estimate Chla and PC in Chao Lake.