The Gaussian model was used to describe the algae vertical profiles and analyze the influence of algae vertical profiles on band ratio algorithm via Hydrolight simulation. It indicated that there was no definite relationship between reflectance of water surface and the algae biomass because of different algae vertical profiles. The algae blooms at the water surface could lead to the failing of retrieval algorithm. Excluding algal bloom case, there were good correlation between band ratio algorithm and chlorophyll-a concentration at 0.25m water depth or averaged chlorophyll-a concentrations at 0~0.25 / 0~0.5m water depth, which is independent on the algae biomass and algae vertical profiles. Comprehensive consideration on chlorophyll-a concentration retrieved from remote sensing algorithm and algae vertical profiles should be an executable approach to obtain algae biomass of inland lakes.