In the past decade, the system of national aquatic germplasm reserves was constructed in China, and over 500 national aquatic germplasm reserves were established in different water type areas. In order to optimize reserve management, we analyzed the distribution pattern of national aquatic germplasm reserves within the water type geographical distribution and key protected species. The following general problems occurred during the construction and management of the reserves. 1) The water type pattern of these reserves was not fully reasonable. The number of inland water reserves were far more than sea reserves, while the mean area of inland water reserves were obviously smaller than sea reserves. 2) There were too few reserves in some basins so that the deficiencies for protecting species occurred, such as some rivers in Southwestern China and Southern China. 3) It was lack of systematic investigation to ensure the list of key protected species. Pelteobagrus fulvidraco was listed as key protected species in 70 reserves, while there were 69 national protected aquatic species excluded from the key protected species list. We should develop a comprehensive plan for aquatic germplasm reserve construction and management, based on a systematic investigation and research, in order to realize the protection and sustainable utilization of aquatic germplasm resources.