The unique geographical conditions in southwestern China lead to a fragile ecological balance and uneven geographical distribution of water resources. This study takes the Aba Tibetan and Qiang Autonomous Prefecture as its research subject, investigating the connection between water resources and the ecological environment in the Aba Tibetan and Qiang Autonomous Prefecture, which is of paramount importance. Given this, the current study constructs the remote sensing ecological index and water footprint for the period spanning from 2000 through 2020, analyses the coordination status of the two by using the coupling coordination degree, and then combines it with a detector to determine the primary drivers impacting the state of the ecological environment. The outcomes reveal that: (1) The ecological environment of the Aba Tibetan and Qiang Autonomous Prefecture gradually improved from 2000 through 2020, and the excellent ecological environment area observed within the study’s scope is primarily focused in the eastern part. The poor ecological environment area is focused mainly in the northwestern part within the study’s scope. (2) The total water footprint of the Aba Tibetan and Qiang Autonomous Prefecture has increased year by year, with agricultural water consumption comprising an immense 78% proportion, dominating the total water footprint. (3) The coupled coordination degree of the remote sensing ecological index and the water footprint shows a rising trend in general, turning from a barely coordinated stage to an intermediate coordinated stage. (4) The geodetector results show that all factor interactions were dual-factor enhancement or nonlinear enhancement, and the WET, NDBSI and NDVI factors contributed the most. The above results can provide important guidance for utilizing water resources and protecting the ecological environment in the Aba Tibetan and Qiang Autonomous Prefecture.