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Pigments in lake surface sediments integrate both benthic and pelagic primary producer composition at the whole-lake ecosystem level. We gathered a comprehensive set of water chemistry, morphometric, physical and biological lake variables, catchment and climate characteristics, and geographical descriptors. We used multiple regressions to relate whole-lake algal pigment concentration to environmental conditions and multivariate statistical analyses to assess the factors most associated with photoautotrophic algal and bacterial community composition. The relative influence of environmental factors and spatial distribution was assessed by variance partitioning analysis among three groups of variables: (1) in-lake factors, (2) external factors, and (3) geographic descriptors. Pigment concentration and community composition were most sensitive to in-lake factors. Pigment-inferred abundance of algae, including cyanobacteria, tended to be highest in shallower systems with high nutrient concentrations, independent of the latitudinal temperature or irradiance gradients. Pigment-inferred community composition was best explained by nutrients and biotic composition (zooplankton and fish communities). Only in maritime temperate lakes did a link with regional location occur due to their low dissolved inorganic nitrogen to soluble reactive phosphorus ratios (1.5 atomic ratio), suggesting nitrogen limitation of phytoplankton growth; accordingly, the sediment pigments revealed cyanobacteria to be the dominant group, although this may also be a consequence of the overall high nutrient levels in these lakes. Despite the large climate gradient covered, in-lake rather than external factors were associated with the patterns observed in pigment concentration (from benthic and pelagic microorganisms) and inferred composition and abundance in these shallow lakes. Our results suggest that pigment assemblages in sediments, which integrate both benthic and pelagic microbial photoautotrophic community and processes, are valuable indicators of changes in shallow (0.75-12 m depth) lake ecosystems.