Stable isotopes in fossil charophyte calcite may record palaeoenvironmental information but at present, very little is known about isotopic records in modern Chara stem encrustations or gyrogonites. This problem is addressed with isotopic data from present-day Chara from a wide spread of freshwater environments in Britain and Ireland. d13C values of stem encrustations from low water flow environments (lakes, ponds, ditches) are more positive than their coexisting gyrogonite values, by between 0.6 and 3.0‰, reflecting microenvironmental metabolic effects caused by photosynthesis. In stronger water flows, where dissolved inorganic carbon is well mixed, stem encrustation d13C values are close to equilibrium. d18O values in Chara stem encrustations are not equilibrium values, being typically offset to isotopically lighter compositions by about 1.5‰ relative to equilibrium by kinetic effects during rapid calcification. Gyrogonite d18O values are less negative than coexisting stem encrustation values by between 0.7 and 1.7‰. There is no clear evidence that gyrogonite d18O or d13C values are influenced by extensive disequilibrium but the data are difficult to interpret further without new experimental studies. Isotopic records in fossil lacustrine Chara marls (mainly stem encrustation calcites) should be interpreted with caution. Environmental records, essentially of relative changes in late summer water temperature or hydrology may be preserved, but these are unlikely to represent true equilibrium values. Gyrogonite calcification probably happens on a timescale of weeks, such that isotopic data represent ‘snapshots’ of the environmental conditions at the time of calcification. The timing of calcification in Chara may itself be variable depending on environment and temperature; it is a major unknown that currently hinders interpretation of isotopic data.