The southern California coastline hosts low-inflow estuaries that have mouths that periodically close. Low-inflow estuaries can become hypoxic and are then often opened mechanically. The consequences of mouth closure and hypoxia (< 2 mg L−1 O2) on macrobenthic densities, species richness, diversity, composition, and biological traits were evaluated for legacy data generated by the Pacific Estuarine Research Lab for Los Peñasquitos Lagoon (LPL) (1991–2006) and Tijuana Estuary (TJE) (1988–2004). LPL closed at least annually and TJE remained open during the study period. Effects were moderated by zone within the estuary (relative to the mouth) and season. Periodic closure in LPL was associated with raised macrofaunal density and diversity, especially at the mouth, and with suppressed seasonality. Closure favored soft-bodied (non-calcified) non-bioturbating, mobile, epifaunal taxa in LPL with planktotrophic development, large branchiae, and no vision. There were more spionid and capitellid polychaetes, Traskorchestia traskiana, Cerithideopsis californica, Tagelus californianus, and phoronids during closure. In contrast, hypoxia (< 2 mg L−1) measured during faunal sampling was associated with lower densities in LPL and different taxonomic composition, but no difference in taxon richness or diversity. There were more corophiid amphipods, small snails, tubificid oligochaetes, Palaemon macrodactylus (shrimp), and Trichorixa reticulata (insects) under hypoxic conditions, and retention of taxa with very large or small bodies and with vision. TJE densities were nearly double those of LPL; taxon richness and diversity (H’) were also higher in TJE. TJE hosted more burrowing, large-bodied, highly calcified taxa with planktotrophic development and no vision than LPL. Differences in composition and traits between the two estuaries disappeared in the middle and upper reaches, where ocean flushing was more limited. Historical long-term monitoring data for benthos, such as the data set analyzed here, offer a valuable baseline for evaluating ecosystem response to changes induced by climate, infrastructure development, contamination, or restoration.