Water trading is aimed at allocating abstracted water more fairly amongst stakeholders, however the direct effect this has on the natural flow regime and consequently on freshwater ecosystems has not been investigated in depth. This paper proposes a novel modelling methodology bringing together habitat and water trading numerical models with statistical models to show how water trading may affect three freshwater species: Fish (Salmo Trutta), Macrophytes (Ranunculus Fluitans) and Benthic macroinvertebrates (Ephemeroptera Beraeidae). Results indicated that trading regimes with environmental constraints to protect the environment had little effect on habitat availability however; trading without such requirements had an impact. Lower habitat suitability scores were apparent under the trading scenarios with lower levels of suitable habitat occurring. However putting these results within the context of natural variability, whilst there was a change in habitat availability, this change is within the natural flow/habitat variance and therefore water trading in the studied catchment is unlikely to impact the overall habitat availability.