Like many areas on the periphery of San Francisco Bay, Hooks Island is classified as California coastal salt marsh.

It is described in a 2020 Santa Clara Valley Water report as an "undisturbed tidal salt marsh" consisting partly of an "estuarine intertidal emergent wetland".

[7] The S. alterniflora, originally introduced to the area in 1973 by an Army Corps of Engineers project to control erosion and restore marshes in the Bay, hybridized with native cord grasses, forming dense growth above ground and a dense root system below; this displaced both surface-dwelling animals and those which lived beneath the mud.

[11] While it is broadly accepted that there are many cats in the San Francisco Bay Area,[12] the extent of their presence in the Palo Alto Baylands (and of their role in the killing of clapper rails) was disputed.

While the city's division manager of open space, parks and golf claimed to have "personally seen feral cats hunt and catch birds in the Baylands Nature Preserve", a volunteer at the Palo Alto Humane Society offered a rejoinder to this claim, stating that "compared to people, the damage feral cats do is minor".