The upper Esopus, located within both the Catskill Park and the New York City watershed, is closely monitored by both the state DEC and the city DEP.
Between the DEC's Forest Preserve holdings, city-owned buffer lands and privately held forested parcels, 99 percent of the land in the upper watershed is forested.
Trout fishermen are also active through groups like Trout Unlimited in working to keep the creek's water clean, although their interests sometimes clash with the city's.

According to the 2007 Upper Esopus management plan compiled by DEP, the Cornell Cooperative Extension and the U.S. Army Corps of Engineers for the Ashokan Watershed Stream Management Program, a joint program run by DEP, Cornell and the Ulster County Soil and Water Conservation District, water quality in that part of the stream is generally good.
Property owners and other stakeholders in the stream expressed concern about flooding risks and attendant erosion problems.
The plan did not find any evidence that floods have become more common in the last century (before Hurricane Irene four years after the report, the record flood for the stream occurred in 1980, with discharges of 65,300 cubic feet per second (1,850 m³/s) recorded above the reservoir and was calculated to be a 40-year flood), despite two heavy floods in the preceding decade.
It recommends that new construction on the creek's flood plain be avoided wherever possible and that flood control measures and warning systems be improved along the length of the upper creek.

The Portal's effect on the creek's fishery is a continuing source of friction.
For a long time after its construction it was believed to have a positive effect on the trout, but after the floods of 1996 some fishermen began complaining that the waters from Schoharie have been too turbid and warm (some calling it "Yoo Hoo Creek"), with the rainbow trout population declining as a consequence.
New York's Department of Environmental Conservation (DEC) says it has found no sign of that, but in 2000 the Catskills chapter of Trout Unlimited, Riverkeeper and some other groups sued the city, arguing the Portal releases into the creek violated the federal Clean Water Act.
After lengthy litigation the city was eventually required to get a state permit for the discharges.
Environmental groups have said the problems would be solved if the Schoharie, like all the other city reservoirs, had a multi-level discharge structure, allowing water to be taken from the less turbid surface as well as the cooler depths.

Boater and tuber user groups depend on releases from the Portal, which can add up to 900 cubic feet per second (25 m³/s) to the creek's flow, to make those activities possible.
Their interests also sometimes differ with the stream's angling community on the question of large woody debris (LWD), such as trees or limbs loosened from the banks during floods.
Those usually come to rest in the stream, sometimes at bridge abutments, creating habitat for trout and other aquatic life but creating navigational hazards.
In 2002 a kayaker and tuber were killed in separate instances as a result of LWD in the stream; both deaths led to lawsuits against property owners.
The management plan has recommended clarifying the liability issues.

Riparian buffers are another issue to be addressed.
Most of the upper Esopus has at least 100 feet (30 m) of buffer on either side, but there are portions with 25 feet (7.6 m) or less and 6.25 miles (10.06 km) have no buffer at all, with revetments shoring up the sides next to the highway or the railroad.
The buffers are mostly closed-canpoy floodplain forests, with mowed lawns making up the remainder.
The upper Esopus, located within both the Catskill Park and the New York City watershed, is closely monitored by both the state DEC and the city DEP. Between the DEC's Forest Preserve holdings, city-owned buffer lands and privately held forested parcels, 99 percent of the land in the upper watershed is forested. Trout fishermen are also active through groups like Trout Unlimited in working to keep the creek's water clean, although their interests sometimes clash with the city's.
According to the 2007 Upper Esopus management plan compiled by DEP, the Cornell Cooperative Extension and the U.S. Army Corps of Engineers for the Ashokan Watershed Stream Management Program, a joint program run by DEP, Cornell and the Ulster County Soil and Water Conservation District, water quality in that part of the stream is generally good. Property owners and other stakeholders in the stream expressed concern about flooding risks and attendant erosion problems. The plan did not find any evidence that floods have become more common in the last century (before Hurricane Irene four years after the report, the record flood for the stream occurred in 1980, with discharges of 65,300 cubic feet per second (1,850 m³/s) recorded above the reservoir and was calculated to be a 40-year flood), despite two heavy floods in the preceding decade. It recommends that new construction on the creek's flood plain be avoided wherever possible and that flood control measures and warning systems be improved along the length of the upper creek.
The Portal's effect on the creek's fishery is a continuing source of friction. For a long time after its construction it was believed to have a positive effect on the trout, but after the floods of 1996 some fishermen began complaining that the waters from Schoharie have been too turbid and warm (some calling it "Yoo Hoo Creek"), with the rainbow trout population declining as a consequence. New York's Department of Environmental Conservation (DEC) says it has found no sign of that, but in 2000 the Catskills chapter of Trout Unlimited, Riverkeeper and some other groups sued the city, arguing the Portal releases into the creek violated the federal Clean Water Act. After lengthy litigation the city was eventually required to get a state permit for the discharges. Environmental groups have said the problems would be solved if the Schoharie, like all the other city reservoirs, had a multi-level discharge structure, allowing water to be taken from the less turbid surface as well as the cooler depths.
Boater and tuber user groups depend on releases from the Portal, which can add up to 900 cubic feet per second (25 m³/s) to the creek's flow, to make those activities possible. Their interests also sometimes differ with the stream's angling community on the question of large woody debris (LWD), such as trees or limbs loosened from the banks during floods. Those usually come to rest in the stream, sometimes at bridge abutments, creating habitat for trout and other aquatic life but creating navigational hazards. In 2002 a kayaker and tuber were killed in separate instances as a result of LWD in the stream; both deaths led to lawsuits against property owners. The management plan has recommended clarifying the liability issues.
Riparian buffers are another issue to be addressed. Most of the upper Esopus has at least 100 feet (30 m) of buffer on either side, but there are portions with 25 feet (7.6 m) or less and 6.25 miles (10.06 km) have no buffer at all, with revetments shoring up the sides next to the highway or the railroad. The buffers are mostly closed-canpoy floodplain forests, with mowed lawns making up the remainder.
Esopus Creek