Despite the overwhelming tendency in paleolimnology to use both planktonic and benthic diatoms when inferring open-water chemical conditions, it remains questionable whether all taxa are appropriate and necessary to construct useful inference models. We examined this question using a 75-lake training set from Quebec (Canada) to assess whether model performance is affected by the deletion of benthic species. Because benthic species are known to experience very different chemical conditions than their planktonic counterparts, we hypothesized that they would introduce undesirable noise in the calibration. Surprisingly, such important variables as pH, total phosphorus (TP), total nitrogen (TN), and dissolved organic carbon (DOC) were well predicted from weighted-averaging partial least square (WA-PLS) models based solely on benthic species. Similar results were obtained regardless of the depth of the lakes. Although the effective number of occurrence (N2) and the tolerance of species influenced the stability of the model residual error (jackknife), the number of species was the major factor responsible for the weaker inference models when based on planktonic diatoms alone. Indeed, when controlled for the number of species in WA-PLS models, individual planktonic diatom species showed superior predictive power over individual benthic species in inferring open-water chemical conditions.