Ecosystems are complex structures with interacting abiotic and biotic processes evolving with ongoing succession. However, limited knowledge exists on the very initial phase of ecosystem development and colonization. Here, we report results of a comprehensive ecosystem development monitoring for twelve floodplain pond mesocosms (FPM; 23.5 m × 7.5 m × 1.5 m each) located in south‐western Germany. In total, 20 abiotic and biotic parameters, including structural and functional variables, were monitored for 21 months after establishment of the FPMs. The results showed evolving ecosystem development and primary succession in all FPMs, with fluctuating abiotic conditions over time. Principal component analyses and redundancy analyses revealed season and succession time (i.e., time since ecosystem establishment) to be significant drivers of changes in environmental conditions. Initial colonization of both aquatic (i.e., water bodies) and terrestrial (i.e., riparian land areas) parts of the pond ecosystems occurred within the first month, with subsequent season‐specific increases in richness and abundance for aquatic and terrestrial taxa over the entire study period. Abiotic environmental conditions and aquatic and terrestrial communities showed increasing interpond variations over time, that is, increasing heterogeneity among the FPMs due to natural environmental divergence. However, both functional variables assessed (i.e., aquatic and terrestrial litter decomposition) showed opposite patterns as litter decomposition rates slightly decreased over time and interpond differences converged with successional ecosystem developments. Overall, our results provide rare insights into the abiotic and biotic conditions and processes during the initial stages of freshwater ecosystem formation, as well as into structural and functional developments of the aquatic and terrestrial environment of newly established pond ecosystems.