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Lacustrine 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. Plain Language Summary: Proxies from sediment cores that reflect the isotopic composition of lake water are commonly used to reconstruct past climate, but understanding the processes affecting lake water isotopes (e.g., the seasonal distribution of precipitation and evaporation) is key to accurate climate interpretations. However, due to accessibility issues, little is known about the seasonal isotopic composition of water in eastern Canadian Arctic lakes. Here, we compile modern lake water isotope (δ18O and δ2H) measurements spanning the eastern Canadian Arctic, with special focus on Baffin Island, collected in 1994–1996 and 2017–2021, to identify regional and seasonal patterns in lake water isotopes. Isotopes from lakes in the southern part of this transect reflect mean annual precipitation with some influence of evaporation. In contrast, lakes in the northern part of this transect reflect summer precipitation isotopes. This latitudinal trend may be caused by vegetation cover: as vegetation becomes less dense northward, relatively more precipitation in a catchment enters the lake as runoff. Despite this trend, there is some variability within each region. Therefore, quantifying lake water isotope seasonality is a critical step toward robust interpretations of lake water isotope proxy records. Key Points: Eastern Canadian Arctic lakes reflect precipitation isotopes with little influence of evaporative enrichmentPatterns in lake water isotope seasonality driven by the ratio of runoff to precipitationGroundwater is an important variable in the lake system that influences lake water isotope seasonality [ABSTRACT FROM AUTHOR]