The Tommelen dataset contains data from bomb crater pools (n=23) at Tommelen nature reserve (Hasselt, Belgium) (122 pools in an area of 12 ha). These ponds have been sampled annually from 2007 until 2012. A subset of the investigated ponds has been dredged in winter 2008. This database comprises biodiversity data on aquatic macro-invertebrates and macrophytes, as well as information on major local environmental variables. Aquatic macro-invertebrates were sampled in 2008 and 2009. Macrophytes data are available for 2007, 2010 and 2012.