Total streamflow across the Muscoot River was last observed at 24 cfs, and is expected to yield approximately 47 acre-ft of water today; about 31% of normal. River levels are low and may signify a drought. Average streamflow for this time of year is 76 cfs, with recent peaks last observed on 2023-07-11 when daily discharge volume was observed at 1,273 cfs.

Maximum discharge along the river is currently at the Muscoot River At Baldwin Place Ny reporting a streamflow rate of 23.8 cfs. However, the streamgauge with the highest stage along the river is the Muscoot River Below Dam At Amawalk Ny with a gauge stage of 8.49 ft. This river is monitored from 2 different streamgauging stations along the Muscoot River, the highest being situated at an altitude of 562 ft, the Muscoot River At Baldwin Place Ny.