The past ∼40 years have seen a geometric increase (5–7% per year) in the size of the lesser snow goose (LSG; Chen caerulescens caerulescens) population and marked spatial expansion of the area they inhabit within the coastal fen ecotype of Wapusk National Park (Hudson Bay Lowlands, northern Canada), raising concerns and uncertainty about the environmental effects of their activities (grubbing of vegetation, soil disturbance, deposition of feces) on the abundant shallow tundra ponds. In this study, we use conventional limnological measurements as well as water and carbon (C) isotope tracers to explore similarities and differences in seasonal patterns of hydrological, limnological, and biogeochemical conditions of 15 shallow coastal fen ponds that currently have minimal (if any) disturbance from the LSG population with one pond (WAP 20) that is subject to substantial LSG activity. Carbon isotope measurements reveal that C cycling at WAP 20 (LSG-disturbed site) is markedly different compared to the other ponds, whereas only small differences were observed in hydrological conditions and concentrations of major nutrients and chlorophyll a of pond water. A mid-summer decrease in C isotope composition of dissolved inorganic carbon (DIC) occurred at WAP 20, likely as a consequence of high pond-water pH and intense C demand by aquatic productivity. These conditions appear to have promoted “chemically enhanced CO₂ invasion,” which causes strong kinetic C isotope fractionation. High C demand at WAP 20 is also suggested by mid-summer ¹³C enrichment in particulate organic matter. In contrast, the ponds with little to no LSG activity exhibited expected seasonal C isotope behavior (i.e., ¹³C enrichment of DIC) under conditions of increasing productivity when C is in relatively low demand. Small differences in nutrient concentrations may be due to rapid uptake by the benthic mat at WAP 20. Data from the low disturbance ponds also provide baseline information for future studies assessing potential effects of LSG.