This dataset contains 1,636 observations of Bosmina species collected from Lake Constance between 1987 and 2019. Each entry includes morphological traits (body size, antennule size, mucro size, eye diameter), reproductive data (egg counts), and metadata (sampling date, associated image file, species classification). Samples were collected using a Clarke-Bumpus sampler (140 µm mesh) during stratified and winter periods, with traits measured from April, June, and August of 19 selected years. Species identification (B. coregoni, B. longispina, and B. longirostris) was based on mucro and antennule morphology, verified by postabdominal claw examination. This dataset provides a valuable resource for investigating long-term ecological and evolutionary dynamics, species turnover, and trait variability in response to environmental changes over three decades.