To better understand the influence of glacier runoff on fjord ecosystems, we sampled oceanographic conditions, nutrients, zooplankton, forage fish and seabirds within 4 fjords in coastal areas of the Gulf Alaska. We used generalized additive models and geostatistics to identify the range of glacier runoff influence into coastal waters within fjords of varying estuarine influence and topographic complexity. We also modeled the response of depth-integrated chlorophyll a concentration, copepod biomass, fish and seabird abundance to physical, nutrient and biotic predictor variables. The effects of glacial runoff were traced at least 10 km into coastal fjords by cold, turbid, stratified and generally nutrient-rich near-surface conditions. Glacially modified physical gradients, nutrient availability and among-fjord differences explained 67% of the variation in phytoplankton abundance, which is a driver of ecosystem structure at higher trophic levels. Copepod, euphausiid, fish and seabird distribution and abundance were related to environmental gradients that could be traced to glacial freshwater input, particularly turbidity and temperature. Seabird density was predicted by prey availability and silicate concentrations, which may be a proxy for upwelling areas where this nutrient is in excess. Similarities in ecosystem structure among fjords were attributable to an influx of cold, fresh and sediment-laden water, whereas differences were likely related to fjord topography and local differences in estuarine vs. ocean influence. We anticipate that continued changes in the timing and volume of glacial runoff will ultimately alter coastal ecosystems in the future.