The evolution of reproductive systems is of critical importance to evolution and yet has been difficult to examine using paleontological information. Recent studies on freshwater "clam shrimp" in both extant and fossil populations have demonstrated that sex can be inferred by quantifying morphological differences of the carapaces. However, the extent of morphological continuity between juveniles and mature phenotypes remains unclear, which, if extensive, would confound the determination of sex ratios from fossil specimens. Herein, we report studies of clam shrimp ontogeny using quantitative morphometric techniques to assess carapace shape change through juvenile and early adult development. Intra- and inter-species ontogenetic variance was captured in three species from two families (Limnadiidae, Cyzicidae), three genera (Paralimnadia, Eulimnadia and Cyzicus), and three breeding systems (dioecy, androdioecy and hermaphroditism) using geometric morphometric analyses to identify and characterize discrete phenotypic stages during ontogeny. With this approach, we successfully discriminated juvenile, male and female/hermaphrodite phenotypes. Additionally, we generated models that described the ontogenetic trajectory of carapace shape as species developed into sexually mature phenotypes. These findings verify the ability of these morphometric techniques to distinguish sex ratios using only carapace shape and, thus, validate the use of fossil spinicaudatans for studies of reproductive system evolution in deep time.