Microalgae may contribute more to salt marsh productivity than realized, underscoring the importance of understanding algal dynamics in such systems. Benthic and planktonic chlorophyll-a (surrogate for total algal biomass), sediment ash-free dry weight, total suspended solids, salinity, and nutrients were examined in intermittently connected marsh ponds in the subtropical Guadalupe Estuary, Texas, USA to determine the effects of hydrologic connections on algal biomass in this system. From May 2005 to May 2006, several high water events resulting in surface water connections between ponds and nearby tidal creeks occurred, followed by disconnection and, at times, pond desiccation. During periods of disconnection, algal biomass was higher in both the benthos and the water column than during connection events when flushing occurred. Since connection events did not increase NO_x, the primary source of dissolved inorganic nitrogen seemed to be nutrient cycling within the ponds. Data at the aggregated level, i.e., chlorophyll-a, indicated this system followed the flood pulse concept. During high water events, algal biomass may be exported to supplement the tidal creek food web (aquatic), whereas during low water events accumulated biomass within the ponds feed the marsh food web (terrestrial), which includes blue crabs (Callinectes sapidus) and the whooping crane (Grus americana).