COI and 18S metabarcoding data from Hidden Lake (Banff National Park, Canada) over two rotenone applications between 2018 and 2020.

Water samples were taken in Hidden Lake at five different time points around two rotenone applications: (i) five weeks prior to the first rotenone application, on July 12 2018; (ii) approximately three weeks after the first application of rotenone, on 7 September 2018; (iii) approximately 10 months after the first rotenone application, on 10 July 2019; (iv) four weeks following the final treatment of rotenone on the 17 September 2019; and (v) one year after the final rotenone treatment, on 19 August 2020. For each time point there is a pelagic, a littoral and a profundal sample. COI and 18S metabarcoding methods were used to produce community data. The objective of this study was to assess the non-target effect of rotenone application (in summer 2018 and 2019) on aquatic communities (i.e. phytoplankton, fungi, zooplankton and benthic macroinvertebrates).