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Two representative methods for quantitative estimation of soil algae, the culture dilution method and chlorophyll a extraction, were compared using soil samples collected from irrigation land in the flood plain of the River Ili, Kazakhstan, where the distribution of soil algae had been studied in the previous year. The estimate by the culture dilution method was almost the same as in the previous year, except for one site, which was enclosed by shrubs of sakusaul, Haloxylon aphyllum (Minkw.) Iljin. The important role of wind in transport of airborne algal cells was pointed out. There was a significant correlation (p < 0.001) between the logarithm of the number of colonies by the culture dilution method and the logarithm of the concentration of chlorophyll a, when data from all samples were analyzed. However, no significant correlation was observed with the data of cropland sites alone. Furthermore, the seasonal variations of both values at each site did not necessarily agree with each other. One reason for the inconsistency may have been the overestimation of chlorophyll a caused by inclusion of litter from vascular plants. Other reasons may relate to differences between the methodologies. The density of soil algae estimated by culture dilution reflects the algal biomass in a certain previous period of time. Therefore, it is suggested that the method is suitable for spatial, but not for seasonal studies.