In this study oxygen and nutrient fluxes and denitrification rates across the sediment-water interface were measured via intact core incubations with a twofold aim: show whether microphytobenthos activity affects these processes and analyse the dispersion of replicate measurements. Eighteen intact sediment cores (i.d. 8 cm) were randomly sampled from a shallow microtidal brackish pond at Tjarno, on the west coast of Sweden, and were incubated in light and in darkness simulating in situ conditions. During incubation O(2), inorganic N and SiO(2) fluxes and denitrification rates (isotope pairing) were measured. Assuming mean values of 18 cores as best estimate of true average (BEA), the accuracy of O(2), NH(4)(+), NO(3)(-) and SiO(2) fluxes calculated for an increasing number of subsamples was tested. At the investigated site, microalgae strongly influenced benthic O(2), inorganic N and SiO(2) fluxes and coupled (D(n)) and uncoupled (D(w)) denitrification through their photosynthetic activity. In the shift between dark and light conditions NH(4)(+) and SiO(2) effluxes (similar to60 and similar to 110 mumol m(-2) h(-1)) and D(n) (similar to5 mumol m(-2) h(-1)) dropped to zero, NO(3)(-) uptake (similar to70 mumol m(-2) h(-1)) showed a 30% increase, while D(w) (similar to20 mumol m(-2) h(-1)) showed an 80% decrease. For O(2) and NO(3)(-) dark fluxes, 4 core replicates were sufficient to obtain averages within 5 - 10% of the best estimated mean, while 10 - 20% accuracy was obtained with 4 - 12 replicates for SiO(2) and > 10 replicates for NH(4)(+) dark fluxes. Mean accuracy was considerably lower for all light incubations, probably due to the patchy distribution of the benthic microalgal community.