Many Recent and fossil freshwater tufa stromatolites contain millimetre-scale, alternating laminae of dense micrite and more porous or sparry crystalline calcites. These alternating laminae have been interpreted to represent seasonally controlled differences in the biotic activity of microbes, and/or seasonally controlled changes in the rate of calcification. Either way, couplets of these microbially mediated alternating calcified laminae are generally agreed to represent annual seasonality. Combined stable isotope (d18O and d13C) and trace element (Mg, Sr, Ba) geochemistry from Recent tufa stromatolites show that seasonal climatic information is available from these calcites. Variability in d18O (and in one case Mg concentration) has been shown to be controlled primarily by stream temperature change, usually driven by solar insolation. In arid climates, seasonal evaporation can also cause d18O enrichment by at least 1‰. Variability in d13C results potentially from: (1) seasonal change in plant uptake of 12C-enriched CO2; (2) seasonal change in degassing of 12C-enriched CO2 in the aquifer system; and (3) precipitation of calcite along the aquifer or river flow path, a process that increases d13C of dissolved inorganic carbon (DIC) in the remaining water. Mechanisms 2 and 3 are linked because calcite precipitates in aquifers where degassing occurs, e.g. air pockets. The latter mechanism for d13C enrichment has also been shown to cause sympathetic variation between trace element/Ca ratios and d13C because trace elements with partition coefficients much greater than 1 (e.g. Sr, Ba) remain preferentially in solution. Since degassing in air pockets will be enhanced during decreased recharge when water saturation of the aquifer is lowest, sympathetic variation in trace element/Ca ratios and d13C is a possible index of recharge and therefore precipitation intensity. High-resolution geochemical data from well-dated tufa stromatolites have great potential for Quaternary palaeoclimate reconstructions, possibly allowing recovery of annual seasonal climatic information including water temperature variation and change in rainfall intensity. However, careful consideration of diagenetic effects, particularly aggrading neomorphism, needs to be the next step.