Shallow lakes are highly sensitive to anthropogenic pressures, and their zooplankton communities—particularly Cladocera—serve as reliable indicators of ecological change. This PhD research investigated two key aspects of Cladocera ecology in Hungarian shallow lakes: (1) the potential unintentional mediation of Cladocera by researchers’ chest waders across differently utilized lakes, and (2) the ecological differences between contemporary and subfossil Cladocera assemblages in a multi-utilized oxbow lake. Field experiments conducted in 13 lakes with varying utilization (oxbow, abandoned fishing, intensive fishing) demonstrated that chest waders can act as effective vectors for Cladocera dispersal, with higher transfer potential in lakes of greater species richness and lower anthropogenic disturbance. Improper cleaning practices risk altering species composition and compromising ecological data integrity. In the Viss Oxbow Lake, comparative analysis of contemporary and subfossil assemblages revealed substantial discrepancies: subfossil samples showed significantly higher species richness, diversity, and abundance, reflecting long-term ecological history, whereas contemporary assemblages reflected the effects of current pressures such as fish predation, agricultural runoff, and recreational activities. Small-bodied species (e.g., Bosmina, Chydorus) dominated disturbed zones, while larger daphnids were more prevalent in protected areas. Overall, the findings highlight the importance of strict sampling protocols to prevent species transfer and demonstrate how lake utilization shapes both present and historical Cladocera community structures. This work provides new insights into zooplankton dispersal mechanisms and reinforces the value of combining contemporary and subfossil data for ecological assessment and lake management.