In many biomes, a variety of different small freshwater habitats, such as pools and phytotelmata can occur together in the same habitat matrix. However, both the biodiversity and the functioning of these ecosystems remain poorly known. Three freshwater habitat types in a tropical West African biodiversity hotspot were studied. The study demonstrated that animal communities in water‐filled tree holes, temporary ponds and granite rock pools were strongly differentiated with exclusive faunas despite their spatial proximity and similar disturbance in the form of seasonal drought. In particular, granite rock pools stood out with a high gamma diversity. Rock pools were also functionally different from the other two habitat types. The three habitats had contrasting predator assemblages, a differential reliance on primary production and different concentrations of available nutrients. The work illustrates that the biodiversity and functions of small temporary freshwater habitats can be strongly differentiated. This shows the unique and potentially complementary roles that these habitats can fulfil in mediating fluxes of energy and nutrients and preserving aquatic biodiversity in landscapes. Temporary aquatic habitats are typically overlooked in conservation policy and local management plans despite being threatened by habitat transformation. In addition, livestock can threaten savanna ponds, wood exploitation can threaten tree holes, and mining and sediment disruption can threaten rock pools. Hence, better knowledge about the ecological functioning of these ecosystems is vital to the implementation of effective conservation strategies.

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