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Abstract Benthic organisms are ideal bioindicators of freshwater inflow effects in bays and estuaries because they are fixed in space and integrate ephemeral processes in the overlying water column over long periods of time. Freshwater inflow regulates water quality, which drives benthic abundance, productivity, diversity, and community structure. Texas estuaries have different long-term characteristic fauna that reflect the long-term average salinity and sediment conditions in each bay system. Within estuary systems, the secondary bays have distinct communities compared to the primary bays because secondary bays are closer to freshwater inflow sources and are more oligohaline and/or brackish in nature than primary bays that are more marine influenced. Similar responses occur within bay types over time when conditions change with droughts, floods, freezes, and major events, such as hurricanes. Bioindicators of freshwater inflow effects include four dominant species: the polychaetes, Mediomastus ambiseta , and Streblospio benedicti ; the bivalve Mulinia lateralis ; and the amphipod Ampelisca abdita . Each of these species is primarily found in secondary bays with similar salinities where abundances are higher than in primary bays. Because of the relationship between prevailing salinity conditions and benthos community structure, assessment of benthic conditions can be used to determine if a “sound ecological environment” exists in a given bay system.