Saanich Inlet has been a highly productive fjord since the last glaciation. During ODP Leg 169S, nearly 70 m of Holocene sediments were recovered from Hole 1034 at the center of the inlet. The younger sediments are laminated, anaerobic, and rich in organic material (1-2.5 wt.% C-org), whereas the older sediments below 70 mbsf are non-laminated, aerobic, with glacio-marine characteristics and have a significantly lower organic matter content. This difference is also reflected in the changes of interstitial fluids, and in biomarker compositions and their carbon isotope signals. The bacterially-derived hopanoid 17 alpha (H),21 beta (H)-hop-22(29)-ene (diploptene) occurs in Saanich Inlet sediments throughout the Holocene but is not present in Pleistocene glacio-marine sediments. Its concentration increases after similar to 6000 years BP up to present time to about 70 mug/g C-org, whereas terrigenous biomarkers such as the n-alkane C-31 are low throughout the Holocene (<51 <mu>g/g C-org) and even slightly decrease to 36 mug/g C-org at the most recent time. The increasing concentrations of diploptene in sediments younger than similar to 6000 years BP separate a recent period of higher primary productivity, stronger anoxic bottom waters, and higher bacterial activity from an older period with lesser activity, heretofore undifferentiated. Carbon isotopic compositions of diploptene in the Holocene are between -31.5 and -39.6 parts per thousand PDB after similar to 6000 years BP. These differences in the carbon isotopic record of diploptene probably reflect changes in microbial community structure of bacteria living at the oxic-anoxic interface of the overlying water column. The heavier isotope values are consistent with the activity of nitrifying bacteria and the lighter isotope values with that of aerobic methanotrophic bacteria. Therefore, intermediate delta C-13 values probably represent mixtures between the populations. In contrast, carbon isotopic compositions of n-C-31 are roughly constant at -31.4 +/- 1.1 parts per thousand PDB throughout the Holocene, indicating a uniform input from cuticular waxes of higher plants. Prior to similar to 6000 years BP, diploptene enriched in C-13 Of up to -26.3 parts per thousand PDB is indicative of cyanobacteria living in the photic zone and suggests a period of lower primary productivity, more oxygenated bottom waters, and hence lower bacterial activity during the earliest Holocene. (C) 2001 Elsevier Science B.V. All rights reserved.