The Condamine catchment lies within the southern part of the Brigalow Belt bioregion and the majority of the catchment falls within the Eastern Darling Downs sub-region. Sattler and Williams (1999) provide a detailed description of the landscapes and regional ecosystems associated with these areas and lists of regional ecosystems are maintained on the EPA's website. Broadly, the Condamine catchment is in an intermediate climatic zone between the moister coastal climate and the drier inland factors, combined with a diversity of landforms and soils, provide habitat for a wide range of native vegetation and fauna.

Major vegetation communities in the Condamine catchment include:

•    Grasslands and grassy eucalypt woodlands on the alluvial plains and surrounding undulating hills of the Condamine River
•    Brigalow/belah open forest on extensive clay plains of the mid to western sections of the catchment
•    Eucalypt open forests and woodlands on undulating and plain areas particularly in the western sections of the catchment
•    Eucalypt woodlands on sandstone hills and residuals
•    Eucalypt woodlands on granite and traprock hills in the south of the catchment.

Approximately 10% of the catchment is covered with mid-dense to dense eucalypt forest and scattered to open eucalypt woodland covers approximately 20% of the catchment. Many of the floodplains were treeless with grass the dominant vegetation. More structured vegetation dominated by trees occurs naturally in the riparian zone.
The historical and ongoing settlement of the Darling Downs, in particular, has led to continued degradation of much of the conservation values of flora and fauna in the Condamine catchment. The floodplain and lowland areas of some shires in the catchment have mostly been cleared of native vegetation (including grasslands and riparian and floodplain woodlands). Within the Condamine catchment, the proportion of remnant vegetation remaining in the shires ranges from about 7 to 30 percent in the east, and 25 to 50 percent in the west. Of this remnant vegetation, up to 70 percent is classified as "endangered" or "of concern" in some parts of the catchment (e.g., Clifton and Cambooya Shires, and Toowoomba City).
There has been no detailed and systematic survey of fauna or flora within the catchment. Specific study areas however show a diverse range of birds, frogs, reptiles and mammals. There are six birds (e.g. Powerful kite), seven reptiles (e.g. Yakka skink), and one frog species (Red and yellow mountain frog) that are classified as rare in the Catchment. The Condamine catchment also contains populations of the endangered bulloak jewel butterfly and the vulnerable imperial blue butterfly. There are four mammals (e.g. Darling Downs hopping mouse) and one bird species (Paradise parrot) that have been declared extinct in the catchment.
There are several rare and threatened plant species recorded for the catchment. Notable examples that occur in remnant native grasslands and eucalypt woodlands include: Digitaria porrecta, Picris evae, Stemmacantha australis, Thesium australe, and Solanum papaverifolium.