In recent years colonies of Japanese knotweed, an invasive species, have been observed along the banks and in buffer areas.
They are considered detrimental to the stream's health since they do not provide shade, are less effective at controlling erosion and, since they grow in thick clusters, impede access to the stream.

Oriental bittersweet, a vine which kills the trees in buffer forests by wrapping itself tightly around them, has also been observed in some areas.
The stream management plan recommends that a comprehensive plan be developed for controlling and eradicating both species, and any others that may be found in the future.

In 2009, the invasive species problem in the buffers was complicated further by the confirmed arrival of Didymosphenia geminata, an algae species commonly referred to as "rock snot", in the creek's waters between Shandaken and the reservoir.
It was the third stream in the state where it has been found, after Batten Kill in Washington County and the East and West branches of the Delaware River in Delaware County, just to the west of the Esopus valley.
The species can clog water intakes but poses no threat to human life.
Trout are more at risk because it often grows over river bottoms, smothering the insect hatches they depend on as a food source.
There is no way at present to eradicate the species; the state has instead advised fishermen to thoroughly clean and disinfect their waders after trips in order to slow its growth and prevent it from reaching other streams.

Research done by the USGS's New York Water Science Center in 2015 found that D. geminata had not appeared to impair the creek's fishery and aquatic life in general significantly, based on periphyton samples taken from 6–20 locations along the upper Esopus on five occasions during 2009–10.
The algae was most abundant during that period at sites just downstream from the Portal.
The authors speculated that the suspended sediment and phosphates in the water may limit blooms.
In recent years colonies of Japanese knotweed, an invasive species, have been observed along the banks and in buffer areas. They are considered detrimental to the stream's health since they do not provide shade, are less effective at controlling erosion and, since they grow in thick clusters, impede access to the stream.
Oriental bittersweet, a vine which kills the trees in buffer forests by wrapping itself tightly around them, has also been observed in some areas. The stream management plan recommends that a comprehensive plan be developed for controlling and eradicating both species, and any others that may be found in the future.
In 2009, the invasive species problem in the buffers was complicated further by the confirmed arrival of Didymosphenia geminata, an algae species commonly referred to as "rock snot", in the creek's waters between Shandaken and the reservoir. It was the third stream in the state where it has been found, after Batten Kill in Washington County and the East and West branches of the Delaware River in Delaware County, just to the west of the Esopus valley. The species can clog water intakes but poses no threat to human life. Trout are more at risk because it often grows over river bottoms, smothering the insect hatches they depend on as a food source. There is no way at present to eradicate the species; the state has instead advised fishermen to thoroughly clean and disinfect their waders after trips in order to slow its growth and prevent it from reaching other streams.
Research done by the USGS's New York Water Science Center in 2015 found that D. geminata had not appeared to impair the creek's fishery and aquatic life in general significantly, based on periphyton samples taken from 6–20 locations along the upper Esopus on five occasions during 2009–10. The algae was most abundant during that period at sites just downstream from the Portal. The authors speculated that the suspended sediment and phosphates in the water may limit blooms.
Esopus Creek