To evaluate the comparability of neo- and paleo-limnology, we made year-to-year as well as seasonal comparisons of contemporary zooplankton data and cladoceran remains in thick (9–42 mm) annual laminations in sediment of Lake Vesijarvi, southern Finland. We calculated the expected annual exuviae production of nine planktonic taxa in the water column using contemporary zooplankton records, and compared the value to the observed net accumulation of their remains in deep sediment for 7 years. Although all of the species studied occur commonly in the lake pelagic zone, deposition of remains differed significantly among taxa. The observed accumulation of three Bosmina species and Chydorus sphaericus was similar to or exceeded expected values, suggesting good preservation of their remains as well as focusing of sediment into the deepest part of the lake. The accumulation of Limnosida and Leptodora remains exceeded expected values several fold, suggesting under-representation of these species in pelagic plankton samples, as well as efficient transportation and spatial averaging of their remains in the sediment. Daphnia, Diaphanosoma, and Ceriodaphnia were clearly under-represented in the sediment due to poor preservation of their remains and use of a 50-μm sieve in sediment processing. Thus, sieving should be taken into account as a possible source of bias. Correlation between relative abundances of all species in the sediment and in the plankton was weak (rs = 0.54, P < 0.001), but for well-preserved species, the correlation was strong (rs = 0.91, P < 0.001). Inter-annual variation in the deposition of remains suggested that resuspension and sediment focusing may vary between years, thus making it difficult to interpret absolute abundances, even though the deepest part of the basin shows clear varve formation and seasonality is well recorded. Detailed study of the uppermost lamination showed the seasonal succession of a cladoceran community within an annual varve as well as differences in the seasonality and intensity of ephippia production among the species. We recommend that results of cladoceran analyses be expressed in several ways (relative abundances, per unit dry weight, per unit organic matter, and as net accumulation values) before drawing final conclusions, as each approach may reveal a different aspect of the deposition process. In addition, sedimentation differences between epilimnetic and hypolimnetic species should be considered in stratified lakes.