The evaluation of measurement uncertainty (MU) is an important method for quantitative determinations derived by microbial cultivation, thus it could further improve the result accuracy. In this study, we aimed to evaluate the MU in total bacteria counts (TBC) in water. Experiments were carried out using Pour Plate Method. The bottom-up approach was used to access the MU of TBC and different mathematical models were set up based on microbial growth principles and test process. Two geometric and five non-geometric progression factors derived from fishbone diagram were selected in these models, especially considering the influence of the bacteria binary fission. The results showed that the calculated value of expanded uncertainty was between 82 and 120CFU/mL when the test result was 100CFU/mL with the 95% confidence level. The geometric progression factor had a greater impact on MU evaluation with almost 80% of contribution, whilst non-geometric progression factor dedicated 60%. Experimental procedures such as sample repeatability, reproducibility and inoculation time should be drawn more attention, thus the accuracy of results could be improved. These innovative models not only reasonable and reliable, but also easy to use. The achievements of this study illustrated that the MU evaluation method could also be applied for analyzing other microbial indicators in water.