Euglenoids lives in hard or soft water habitats of varied pH and light levels - mainly marshes, swamps, bogs, mires, and other wetlands with an abundance of decaying organic matter. Populations thrive under high nutrient levels, and are therefore useful bioindicators of such conditions.
The decomposing organics release short chain fatty acids, sugars, vitamins B1 and B12, and the other organic compounds needed by euglenoids. This group may also be found in marine or brackish sand and mud flats, farm ponds, the digestive tracks of small aquatic creatures, and the interfaces of air and water, and water and sediment.
The cells are sometimes preyed upon by parasitic chytrids or are consumed by herbivores such as the euglenoid Peranema. Euglena has lost its phagotrophic abilities and instead photosynthesizes as its sole food source. Certain euglenoids, especially some species of Euglena, can survive for long periods in harsh environments such as desert cryptogamic crusts or very acidic waters and can tolerate rapid increases in salinity.