Regulatory agencies often rely on paleolimnological studies for models that predict variables pertinent to nutrient loading or to public perception. Limitations of statistical approaches often pose significant challenges. We present a case study from Florida USA that involves diatom-based inference models derived from two calibration sets. Spatial autocorrelation conclusions differed with methods and approaches, and h block cross validation was unduly pessimistic. Calibration sets and temporal sets represent fundamentally different populations. The accuracy and precision of temporal inferences for specific lakes can be affected by site-specific factors, and are not likely to be known with the certainty suggested by models. Error terms can provide a false sense of knowledge about the reliability of inferences for temporal samples. Broad error terms for limnetic total phosphorus models have little or no utility in any event. Limnetic total P models can perform poorly when applied to N-limited lakes. Transfer functions should be regarded more as qualitative indicators of past water quality rather than methods with known precision, and more emphasis should be placed on multiple lines of evidence and ecological interpretations.