The EA say they will be deploying equipment to continuously monitor water in the river system that includes the catchment of the River Lugg, which flows through the border town of Presteigne and meets its main tributary, the River Arrow, to the south of Leominster.
Monitoring is also being carried out on the River Frome, which rises at Bromyard.
A spokesman for the Environment Agency said: "We are aware of brown algae developing in the River Wye in Herefordshire.
"Analysis confirmed that there was a diatom bloom present from the family stephanodiscaceae.
"These diatoms are a fairly common occurrence in spring in large rivers, causing a brown discolouration to the water."
The substance can irritate fish gills and anglers have been put on alert to spot the signs of brown algae, which is not toxic.
Problems with algae can be made worse by rising temperatures and the EA says rising nutrient levels, such as those from agricultural pollution, increase the chances of algae developing.
Algae are plants that change the water chemistry and are harmful to the river habitat as they block sunlight from reaching plants in the water and use up oxygen in the water at night, which can suffocate fish and other wildlife.
Anglers have been advised to avoid fishing if the water temperature exceeds 20°C by mid-morning.
The EA spokesman said fish should be kept in the water for unhooking, and they should not be removed from the water to take photos of.
"Keeping a fish in the air, even for a few seconds, can greatly reduce its chances of surviving after capture and going on to spawn successfully," said the EA spokesman.
Water quality will be monitored throughout the summer months, until the end of September.
Members of the public have also been asked to report dead fish to the Environment Agency's 24-hour incident hotline on 0800 80 70 60 or email firstname.lastname@example.org to report.
They can also use those contact details to report suspect pollution or witness impacts due to an algal bloom.
Algal blooms occur during periods of warm, settled, dry weather.
There are many types of algae. Some pose a small risk to human and animal health through direct contact with them, although these are usually blue-green algae which are more commonly associated with still waters rather than watercourses like the River Wye.