Bay environments differ in productivity and species composition from open waters. Transects of surface sediments in Lake Washington (Seattle) reveal significant morphological gradients in the small pelagic cladoceran Bosmina longirostris. In all bays examined, these bosminids range from shorter featured clones nearshore to longer featured clones offshore. However, because bays constitute such a limited areal extent of the lake (4.9%), only 2.3% of remains in midlake sediments came from bay populations. A core taken from midlake waters indicates nearly uniform long‐featured morphology of offshore Bosmina over the past 80–125 yr. The localized deposition of remains in bays underscores that biodiversity surveys of large lakes need to include bays in addition to open‐water samples.Clarifying how abundant cladoceran remains are produced, transported to, and preserved in sediments is crucial for interpreting historical sequences. A simple vertical model, derived from molting and death schedules, accurately predicts relative seasonal fluxes for remains at a midlake site (r = 0.9−0.95). However, the absolute flux is low, <7% of the expected rate, suggesting substantial loss through decomposition and fragmentation. Use of abundant cladoceran microfossils to reconstruct species‐specific or general secondary production requires careful calibration studies, although the potential dividends are great.