Recent biological and chemical testing indicates water quality has been improving in the upper watershed (above the village of Fishkill) but remains low below it, particularly in the creek within the city of Beacon, with an improvement just above the estuary. There are 25 State Pollution Discharge Elimination System (SPDES) permits issued by the state Department of Environmental Conservation (DEC) within the watershed, four of which are on the Fishkill itself. A further 64 permits have been issued for groundwater discharge.