With half of the rivers in England and Wales already at 50 per cent of their normal flows for the time of year, the groups are alarmed that further increased abstraction could have disastrous consequences.
Many fish rescues have taken place throughout the summer as oxygen levels in certain stretches dropped catastrophically due to a combination of factors.
Slower flows than usual resulted in water being less aerated by normal turbulence, a condition exacerbated by the rising temperatures as the endless sun during the recent heatwave shone on the sluggish rivers.
But the effect goes much wider. Insects and micro- organisms have also been affected when there has been a bearing on the whole food chain. In particular the otter, a species which had only recently begun to re-establish itself, is likely to suffer if the stocks of fish go down as well as river levels.
Breeding birds such as the bittern, redshank, snipe and kingfisher are also at risk as marshes and wetland dry out when water is removed for consumption.
According to the Royal Society for the Protection of Birds there are up to 60 rivers seriously affected by normal abstraction directly or from nearby acquifers.
Similarly, there are about 40 Sites of Special Scientific Interest (SSSI) at risk. Twenty river SSSIs are suffering extremely low flows or have completely dried out in their upper reaches, according to English Nature.
Another 20 fenland SSSIs in East Anglia are also vulnerable because of abstraction from bore-holes, the danger being that if they dry out the land will be reclaimed by grass and eventually woodland which will alter the ecological balance of the area.
Graham Wynne, the RSPB director of conservation, said: "It is not enough for the Government to seek quick-fix solutions to the problems caused by the current drought. There is now a clear opportunity for a long-term approach to managing the demand for water, which reduces damage to rivers and other wetlands."