Although brackish marsh has been the subject of decades of research, tidal freshwater regions are still poorly understood. To provide insight into spatial and temporal dynamics of nutrients, physical conditions, and the plankton community in freshwater tidal habitat, we investigated from 2011 to 2014 a remnant freshwater tidal slough complex located in the Sacramento-San Joaquin Delta region of the San Francisco Estuary. Our results suggest that the tidal slough complex showed different seasonal nutrient, physical, and biological conditions when compared to a relatively homogenous adjacent large river channel, the Sacramento River. The tidal slough complex also showed substantial spatial variability in habitat conditions compared to nearby main river channels. Nutrient dynamics in the tidal slough complex appear to be driven by a complex suite of factors, including inflow from upstream tributaries and tidal flows from the downstream reach of the Sacramento River. Chlorophyll a in the tidal sloughs responded more strongly to upstream flow pulses than other environmental variables. The tidal slough complex generated significantly higher levels of chlorophyll a than other freshwater regions of the Delta. The 2011 and 2012 results were especially notable because unusually large flow pulses through the tidal slough complex appear to have contributed to rare phytoplankton blooms in downstream areas of the Delta during the fall months. Moreover, the 2012 flow pulse stimulated higher trophic levels, because significantly higher levels of zooplankton were in the tidal slough complex after the flow event. These results have important implications for our understanding of the functioning of freshwater tidal habitat, and for the design of potential restoration projects in these regions.