| Summary: | (1) Background: Paleolimnological studies use sediment cores to explore long-term changes in lake ecology, including occurrences of harmful cyanobacterial blooms. Most studies are based on single cores, assuming this is representative of the whole lake, but data on small-scale spatial variability of microbial communities in lake sediment are scarce. (2) Methods: Surface sediments (top 0.5 cm) from 12 sites (<i>n</i> = 36) and two sediment cores were collected in Lake Rotorua (New Zealand). Bacterial community (16S rRNA metabarcoding), <i>Microcystis</i> specific 16S rRNA, microcystin synthetase gene E (<i>mcyE</i>) and microcystins (MCs) were assessed. Radionuclide measurements (<sup>210</sup>Pb, <sup>137</sup>Cs) were used to date sediments. (3) Results: Bacterial community, based on relative abundances, differed significantly between surface sediment sites (<i>p</i> < 0.001) but the majority of bacterial amplicon sequence variants (88.8%) were shared. Despite intense MC producing <i>Microcystis</i> blooms in the past, no <i>Microcystis</i> specific 16S rRNA, <i>mcyE</i> and MCs were found in surface sediments but occurred deeper in sediment cores (approximately 1950′s). <sup>210</sup>Pb measurements showed a disturbed profile, similar to patterns previously observed, as a result of earthquakes. (4) Conclusions: A single sediment core can capture dominant microbial communities. Toxin producing <i>Microcystis</i> blooms are a recent phenomenon in Lake Rotorua. We posit that the absence of <i>Microcystis</i> from the surface sediments is a consequence of the Kaikoura earthquake two years prior to our sampling.
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