Lakes in cold zones have common characteristics of long frozen periods and fragile water ecosystems. More and more lakes in cold zones have been experiencing water quality deterioration due to eutrophication with climate change and human activities. Lake Hulun is located in the cold zone of northern China, in which Cyanobacterial blooms frequently occur. The excessive nutrient input with inflowing river water and the change in lake hydrodynamic condition might be the main factors affecting this. To obtain a better understanding of the effects, the input loads of nutrients from the inflowing rivers were analyzed. A field test of freezing concentration combined with microbial activity regulation was carried out at a river–lake confluence. The results showed the following: (1) Lake Hulun receives a large amount of nitrogen and phosphorus pollutants from river runoff every year, and the water quality of these river is inferior Grade V, which greatly increases the difficulty in ecological purification of cold zone lakes. (2) The microbial activity control technology has a high purification rate for water during the unfrozen period. The order of purification rates for each hydrochemical index was TP > TN > COD > NH4+-N, and the purification rates of TN and COD were between 35% and 36%. Compared with the water before purification, the water quality grade improved from Grade V to Grade III. (3) The composite technology of freezing concentration–microbial activity regulation has a general water purification rate during the frozen period. Under the low-temperature condition, the TN and COD nutrient fluxes in the water were reduced by 9.38% and 9.36%, respectively. After purification, the water quality grade of the ice body was above Grade II, and the water under the ice layer was above Grade IV, which was one grade higher than the water quality grade of the original lake water. This water treatment and purification process is a green, low-energy consumption, and low-cost technology. This study can provide reference for the integration and demonstration of lake water ecological governance and water resources security technology in cold and arid regions. It is beneficial to the sustainable development of the lake.