The invention relates to a method for estimation of bacterial number in water by particle count in water, and the method belongs to the fields of drinking water processing and sanitation. First, for drinking water with turbidity lower than 1NTU, surface water in rivers and lakes, underground water, and industrial water with turbidity lower than 0.5NTU, a particle calculating instrument is used to determine particle count in certain particle size scopes, and determine bacteria number simultaneously; a certain amount of data is accumulated to satisfy statistical requirement after a plurality of detections, and function relationship between bacterial number and particle count in the certain particle size scope is established; and the function relationship is used to determine bacterial number in water from particle count in the certain particle size scope which is determined by the particle calculating instrument. The estimation method in the invention is simple and fast, can be used for on-line measurement, can determine conventional microorganism indexes such as the total number of bacterium colony, the total number of coliform group bacteria and the like, and can be used for determination of specific microbes such as cryptosporidium, giardia and the like.