Shells of the helicid Cepaea nemoralis were studied using taphonomic, isotopic and morphometric measurements to estimate late glacial–Holocene (~ 12.1–6.3 cal ka BP) environmental conditions in northern Spain. Higher taphonomic alteration among Holocene shells suggests lower sedimentation rates or higher shell-destruction rates than during glacial conditions. Shells preserved the aragonitic composition despite differing degree of skeleton damage. Shell δ13C values were − 10.3 ± 1.1‰, − 8.2 ± 2.3‰, and − 7.3 ± 1.6‰ for modern, Holocene and late-glacial individuals, respectively. Higher δ13C values during the late-glacial and some Holocene periods imply higher water stress of C3 plants and/or higher limestone contribution than today. Intrashell δ13C values were higher during juvenile stages suggesting higher limestone ingestion to promote shell growth. Shell δ18O values were − 1.1 ± 0.7‰, − 0.9 ± 0.8‰ and − 0.1 ± 0.7‰ for modern, Holocene and late-glacial specimens, respectively. A snail flux-balance model suggests that during ~ 12.1 − 10.9 cal ka BP conditions were drier and became wetter at ~ 8.4 − 6.3 cal ka BP and today. Intrashell δ18O profiles reveal that glacial individuals experienced more extreme seasonality than interglacial shells, despite possible larger hibernation periods. Shell size correlated positively with δ18O values, suggesting that growth rates and ultimate adult size of C. nemoralis may respond to climate fluctuation in northern Spain.