Anthropogenic modifications of estuarine environments, including shoreline hardening and corresponding alteration of water quality, are accelerating worldwide as human population increases in coastal regions. Estuarine fish species inhabiting temperate ecosystems are adapted to extreme variations in environmental conditions including water temperature, salinity, and dissolved oxygen across seasonal, daily, and hourly time scales. The present research utilized quantitative sampling to examine the spatiotemporal distribution of shore-zone estuarine fish species in association with four unique shoreline types across a range of water temperature and dissolved oxygen conditions. Fish were collected from the intertidal and shallow subtidal region of four shoreline types, Spartina alterniflora marsh, Phragmites australis marsh, riprap, and bulkhead, in the summer and fall of 2009 and 2010. Analyses were performed to (1) compare mean fish density among shoreline types across all water conditions and (2) explore relationships of the complete fish assemblage, three functional species groupings, and two fish species (Fundulus heteroclitus and Menidia menidia) to unique shoreline/water conditions. Significantly greater mean fish densities were found along S. alterniflora shorelines than armored shorelines. Several metrics including fish density, species richness, and occurrence rates suggest S. alterniflora shorelines may serve as a form of refuge habitat during periods of low dissolved oxygen and high temperatures for various species, particularly littoral-demersal species including F. heteroclitus. Potential mechanisms that could contribute to a habitat providing refuge during adverse water quality conditions include tempering of the adverse condition (decreased temperatures, increased dissolved oxygen), predation protection, and increased foraging opportunities.