To gain insight into the importance of the benthos in carbon and nutri
ent budgets of Boston Harbor and surrounding bays, we measured sedimen
t-water exchanges of oxygen, total carbon dioxide (DIC), nitrogen (amm
onium, nitrite + nitrite, urea, N2O), silicate, and phosphorus at seve
ral stations in different sedimentary environments just prior to and s
ubsequent to cessation of sewage sludge disposal in the harbor. The ra
tio of the average annual DIC release to O-2 uptake at three primary s
tations ranged from 0.84 to 1.99. Annual average DIC:DIN flux ratios w
ere consistently greater than predicted from the Redfield ratio, sugge
sting substantial losses of mineralized N. The pattern was less clear
for P: some stations showed evidence that the sediments were a sink fo
r P while others appeared to be a net source to the water column over
the study period. In general, temporal and spatial patterns of respira
tion, nutrient fluxes, and flux ratios were not consistently related t
o measures of sediments oxidation-reduction status such as Eh or disso
lved sulfide. Sediments from Boston Harbor metabolize a relatively hig
h percentage (46%) of the organic matter inputs from phytoplankton pro
duction and allochthonous inputs when compared to most estuarine syste
ms. Nutrient regeneration from the benthos is equivalent to 40% of the
N, 29% of the P, and more than 60% of the Si demand of the phytoplank
ton. However, the role of the benthos in supporting primary production
at the present time may be minor as nutrient inputs from sewage and o
ther sources exceed benthic fluxes of N and P by 10-fold and Si by 4-f
old. Our estimates of denitrification from DIC:DIN fluxes suggests tha
t about 45% of the N mineralized in the sediments is denitrified, whic
h accounts for about 17% of the N inputs from land.