Northern high-latitude glaciers impact nearshore marine ecosystems through the discharge of cold and fresh waters, including nutrients and organic matter. Fishes are important integrators of ecosystem processes and hold key positions in the transfer of energy to higher trophic positions in such systems. This study used a natural gradient in space and time, including watershed glacial cover (0–60%) of five adjacent estuaries and three sequential discharge periods (pre-peak, peak, post-peak) in the northern Gulf of Alaska (Kachemak Bay) to test whether differences in glacial cover of watersheds upstream of estuaries affect dietary resource use of nearshore fishes. Dietary resource use was assessed using stomach content and stable carbon and nitrogen isotope analyses to determine fish diet composition and trophic niche width. Crescent gunnel (Pholis laeta), a mostly sedentary species, was our focal species for comparisons across estuaries and discharge periods. Discharge period had a greater influence on diet composition and trophic niche width of crescent gunnels than watershed glacial coverage. Niche width of crescent gunnel was larger during the post-peak discharge period compared to pre-peak and peak periods, coincident with a shift in prey spectrum. However, watershed glacial cover was not a suitable predictor of niche width of crescent gunnel. Trophic resource use was also considered along this glacial cover gradient for two other fish species, Pacific staghorn sculpin (Leptocottus armatus) and starry flounder (Platichthys stellatus), but within the post-peak discharge period only. These species exploited a larger prey base compared to crescent gunnel, likely due to their greater mobility. Similar to crescent gunnel, there were no relationships in trophic niche width associated with watershed glacial coverage for these other species during the post-peak discharge period. Instead, trophic resource use of these three nearshore fish species was influenced by a more complex set of dynamic environmental variables (salinity, temperature, turbidity, and discharge), as well as static watershed characteristics, especially vegetation cover. Such drivers can act through changes in metabolic rates, modulating foraging strategies and trophic connectivity, as well as terrestrial nutrient delivery to support estuarine production. The environmental conditions associated with the glacially influenced estuaries during our study period (2020−2021) seemed within a range that allowed nearshore fishes to maintain energy pathways and prey bases across these estuaries, but it is unknown how these estuarine food webs may be influenced in years of extreme conditions such as during heat waves, droughts, or floods.