Shallow coastal bays such as those along the U.S. east coast are particularly vulnerable to changes in coastal zone activities that result in accelerated nutrient delivery rates. A major challenge in these systems is to understand how increased nutrient loading affects ecosystem structure and function. Much of the benthos in these shallow bays is illuminated by sunlight; as a result, benthic autotrophs such as seagrass, benthic microalgae (BMA) and macroalgae play an integral role in nutrient cycling. It has been hypothesized that increased nutrient loading will shift the autotrophic community structure from slow-growing seagrass to ephemeral “nuisance” macroalgae.  The impact of this change in autotrophic structure on sediment biogeochemical cycling is not well understood.  Investigating pathways of carbon (C) and nitrogen (N) flow through individual compartments within the sediment microbial community has previously proved challenging due to methodological difficulties.  It is now possible using stable istotopes and microbial biomarkers such as fatty and amino acids to track C and N flow through individual micorbial pools.  We conducted a series of mesocosm experiments using novel bulk and compound-specific isotopic methods to: 1) track the pathways of dissolved inorganic C and N through the sediments in the presence and absence of macroalgae, and 2) track the fate of macroalgal-bound C and N within the sediments after a simulated die-off event.  Our results suggest that while growing, macroalgae compete with BMA for nutrients and light, diminishing their role in nutrient cycling. This translates to diminshed C and N uptake by sediment bacteria, suggestive of a close coupling between the BMA and bacterial communities.  After macroalgae die, approximately 30% of the macroalgal C and N is transferred to the sediments, where it is decomposed by bacteria and subsequently transferred to BMA.  The remainder is decomposed in the water column, which may fuel eutrophication and further degrade water quality.  Overall, macroalgal retention of C, N is only temporary, and macroalgal blooms decrease retention of C and N within the sediments, which could serve as a positive feedback in already eutrophied systems.