Oxygen isotope (δ18O) measurements on the exoskeletons of aquatic insects can be used to reconstruct changes in the δ18O of ambient water and, indirectly, to infer the climate and environmental conditions at the time of tissue synthesis. Prior to stable isotope analysis, it is often necessary to chemically pretreat insect remains to remove allochthonous organic and inorganic compounds without altering the δ18O signature. We tested the effectiveness and impact of duration of exposure to a buffered 2 M ammonium chloride (NH4Cl) solution for removing carbonates at neutral pH from chironomid head capsules, water beetle sclerites and marine crab remains prior to stable isotope analysis. Immersion in NH4Cl for 24 h efficiently removed the effect of carbonates with no long-term effects of prolonged exposure observed. Furthermore, we assessed the variability in δ18O values within and between individual sclerites (exoskeleton parts) of both modern and fossil water beetle remains. Both modern and fossil specimens had similar intra-sclerite variability in δ18O values (~ 2‰ range). In contrast, modern specimens had much smaller inter-sclerite variability (< 0.9‰ range) compared with fossil specimens from the same sample (up to 10‰ range). The high inter-sclerite variability observed in fossil material likely results from the nature of fossil material: a mix of sclerites from a 1–2–L sample bin, originating from different individuals that may have existed at different times and under different environmental conditions. We therefore recommend that material to be analysed for stable isotopes be sampled at high temporal resolution to reduce uncertainties in paleotemperature estimates derived from water beetle δ18O records.