Algal remains (pigment concentrations, diatom frustules) and organic matter sources (d 15 N, d13 C) in surface sediments (0Á2 cm) were quantified and related to environmental gradients in Doubtful Sound, Fiordland, New Zealand. Sedimentary pigment concentrations, in particular diatoxanthin and fucoxanthin (diatom biomarkers) were elevated near Malaspina Reach, which experiences greater incident irradiance and mixing of silica-rich freshwater with nutrient-rich marine water. In contrast, diatom frustules were recovered in low concentrations in deep basins including Malaspina Reach, most likely related to dissolution and grazing. Spatial variability in pigments in Doubtful Sound was mainly correlated with light conditions (incident irradiance, chromophoric dissolved organic matter). By contrast, diatoms were principally correlated with salinity gradients (effective freshwater depth) and water column stratification (mixing). This study highlights the importance of using complementary sedimentary proxies when reconstructing algal abundance and community composition in fjord environments.