I addressed the effects of taphonomic and early diagenetic processes on the isotope composition of cladoceran remains, using both experimental and field approaches. An experiment was designed to mimic the conditions encountered by cladoceran remains when they settle through the water column and are buried in the sediment. Cladoceran exoskeletons were incubated for 4 months in oxic or anoxic water, and in sediment. Changes in their carbon (C) and nitrogen (N) content and isotope compositions were measured. Most changes in isotope composition of exoskeletons took place when they settled through the water column. Once buried in the sediment, however, the δ13C and δ15N values of cladoceran exoskeletons did not undergo further change. Taphonomic processes resulted in an increase in δ13C and δ15N of the cladoceran remains and this was related to microbial degradation, which selectively removed isotopically light C and N compounds from the remains. For δ13C, changes were minimal (<1‰) and occured within the first 3 months. Taphonomic effects on δ15N were larger, from +2 to +5‰, and occurred within the first 2–3 weeks. These effects depended on incubation conditions and were greater in anoxic waters than under oxic conditions. Monthly changes in the isotope composition of sedimenting cladoceran exoskeletons were also recorded in the field using sediment traps, and were compared to the isotope composition of the living cladoceran community. The isotope composition of sedimenting remains displayed values consistent with those that might be expected, considering the effects of taphonomic processes observed in the experiment. Because C and N in cladoceran exoskeletons might involve a different isotope routing, the δ15N value of the remains provides an annual record of the value in the parent community, with a 1-month delay, while δ13C of remains essentially reflects that of the parent community during the period of lake thermal stratification. These findings provide insights into paleolimnological interpretation of isotopic changes in cladoceran remains from sediment cores.