Although the color of cyanobacteria is a very informative characteristic, no standardized protocol has, so far, been established for defining the color in an objective way, and, therefore, direct comparison of experimental results obtained by different research groups is not possible. In the present study, we used colorimetric measurements and conventional statistical tools to determine the effects on the measurement of the color of cyanobacteria, of the concentration of the microorganisms and their moisture content, as well as of the size of the target area and the minimum number of measurements. It was concluded that the color measurement is affected by every factor studied, but that this can be controlled for by making at least $10\text{\hspace{0.17em} consecutive measurements}/9.62{\mathrm{cm}}^2$ at different randomly selected points on the surface of filters completely covered by films of cyanobacteria in which the moisture contents are higher than 50%.