In response to the prominent contradiction in water resources and severe damage to water ecosystems in the Beijing-Tianjin-Hebei Region, a comprehensive evaluation index system for water resources collaborative protection status based on “quantity-quality-domain-connectivity-biology” was constructed according to the connotation of water resource collaborative protection, and a comprehensive evaluation of the water resources collaborative protection status in the Beijing-Tianjin-Hebei Region was conducted. The results show that the scores of water resources collaborative protection in the Beijing-Tianjin-Hebei Region in 2018 were 59.6,46.1, and 56.8, respectively, which are lower than the national level of 64.8. There is still significant room for improvement in water resources protection work. Based on the evaluation results, the weakness in the water resources collaborative protection status in the Beijing-Tianjin-Hebei Region are identified, and it is found that there are certain gaps in the evaluation results of each dimension compared with the national average level. Among them, the evaluation score of the water quantity dimension is significantly lower than the national average level, and the contradiction of water resources shortage is prominent. Effectively solving the problems of ecological base flow being squeezed and uneven groundwater extraction and replenishment is the key to achieving collaborative protection of regional water resources.