Supporting information

Table S1: List of sites where sediment was collected at Lake Way for the two experiments carried out in this study.

Table S2: Custom COI and 16S sequences generated from Lake Way as part of this study.

Table S3: Summary of reads after each filtering stage for both experiments and assays utilised in this study. Data for “eDNAFlow”, “Unassigned reads”, “Decontamination” and “Non‐target” are presented as reads (unique ZOTUs). The “Non‐target removed” is the reads and ZOTUs present in the final dataset. Mean read depth ± standard error and number of samples (n = X) in the final dataset of each assay for either experiment.

Table S4: List of taxa detected using fwh and Crust16S metabarcoding assays with samples processed by sugar‐flotation (Sugar) and standard sediment DNA extraction (Sediment) in Experiment 1. Numbers reflect the number of biological replicates that a species was detected in at a site.

Table S5: Summary of the mean number of reads per sample and the number of samples which passed all data filtering steps split by assay and the four sediment weight categories tested in Experiment 2.

Table S6: Taxa detected in Experiment 2 split by assay (Crust16S, fwh), sediment weight class and site. Numbers reflect the number of biological replicates that a species was detected in at a site.

Table S7: Abiotic data collected during the rehydration trials for Experiment 2. Wetting event refers to either the initial wetting cycling (W1) or the second round of re‐wetting (W2). EC = electrical conductivity and DO = dissolved oxygen.