Operational data from nine dairy wastewater plants in Wisconsin were collected and analyzed to determine reasons for frequent deterioration of biological phosphorus removal (BPR) efficiency and to optimize BPR for various wastewater treatment processes. Several major factors affecting BPR were identified from the data obtained from dairy wastewater treatment plants. First, many dairy wastewater treatment plants suffer low F/M ratios during off-days, leading to sludge bulking and unstable and poor BPR efficiency. Most dairies do not have an equalization tank or the size is inadequate to alleviate the fluctuation in flow and organic loading. Second, many dairy wastewaters are nutrient deficient. Currently, there are few plants adding ammonia or urea steadily and automatically. Third, many dairies have a severe pH swing within a matter of hours. Fourth, seasonal temperature variations are also found to have a significant effect on the microbial population, leading to the decrease in BPR efficiency. Fifth, frequent chemicals spills, notably brine solution, led to poor BPR as well as decreased COD removal efficiency. Last, the fluctuation in flow, organic loading, and pH magnified the impact to small anaerobic/anoxic tanks compared with large conventional continuously-stirred tank reactors. Laboratory-scale tests confirmed the effects of the COD/P ratio and pH on BPR efficiency. As the influent COD/P ratio increased, the phosphorous release during the anaerobic stage increased, resulting in improved BPR efficiency. When influent pH was greater than 8.5 under the condition tested, microorganisms lost their stability in a bench-scale batch test. Several suggestions for achieving stable and efficient BPR are provided.