Fisheries that target sedentary shellfish present several challenges for deriving management reference points. Stock-recruit relationships often function at a relatively large spatial scale, with planktonic dispersal of eggs and larvae connecting discrete settlement areas, but postsettlement demographics are heterogeneous among local settlement areas. Another challenge is that information on age composition is not available for many invertebrates. Case studies of sedentary shellfish fisheries demonstrate a series of methods for estimating reference points. Biomass dynamics models may be an option for some data-limited fisheries, but inferences of metapopulation productivity can be confounded by serial depletion, so fishery and survey data should be explored for spatial patterns. Yield-per-recruit and eggs-per-recruit models can be size-based and spatially stratified. Demographic models of the full life cycle can integrate regional recruitment processes and postrecruitment processes at smaller spatial scales. Although metapopulation dynamics and spatial heterogeneity in postsettlement demographics can be accounted for in reference points, achieving the optimum yield of sedentary shellfish is largely conditional on managing spatial fishing patterns.