AbstractLacustrine δ2H and δ18O isotope proxies are powerful tools for reconstructing past climate and precipitation changes in the Arctic. However, robust paleoclimate record interpretations depend on site‐specific lake water isotope systematics, which are poorly described in the eastern Canadian Arctic due to insufficient modern lake water isotope data. We use modern lake water isotopes (δ18O and δ2H) collected between 1994–1997 and 2017–2021 from a transect of sites spanning a Québec‐to‐Ellesmere Island gradient to evaluate the effects of inflow seasonality and evaporative enrichment on the δ2H and δ18O composition of lake water. Four lakes near Iqaluit, Nunavut sampled biweekly through three ice‐free seasons reflect mean annual precipitation isotopes with slight evaporative enrichment. In a 23° latitudinal transect of 181 lakes, through‐flowing lake water δ2H and δ18O fall along local meteoric water lines. Despite variability within each region, we observe a latitudinal pattern: southern lakes reflect mean annual precipitation isotopes, whereas northern lakes reflect summer‐biased precipitation isotopes. This pattern suggests that northern lakes are more fully flushed with summer precipitation, and we hypothesize that this occurs because the ratio of runoff to precipitation increases with latitude as vegetation cover decreases. Therefore, proxy records from through‐flowing lakes in this region should reflect precipitation isotopes with minimal influence of evaporation, but vegetation changes in lake catchments across a latitudinal transect and through geologic time may influence the seasonality of lake water isotopic compositions. Thus, we recommend that future lake water isotope proxy records are considered in context with temperature and ecological proxy records.