Zooplankton play an important role in the pelagic food web as a mediator of nutrient and energy fluxes. Understanding factors determining zooplankton abundance, composition, and dispersal provides information needed for improving plankton dynamic predictions and enhancing effective water resource management and biodiversity conservation. We studied zooplankton dispersal and identified factors influence zooplankton composition and abundance under a unique in situ environment with four connected water types from the natural river to a man-made main canal, then interior canal-web, and finally lake that have different flow regimes. We found that, after seven years creation of the water system and zooplankton community development, the main canal, interior canal-web, and lake had 53%–64% zooplankton taxa similar to their water origin river but that each water type was represented and dominated by different zooplankton taxa. Our optimal model identified three key local factors that affected the difference in zooplankton abundance and composition among the four water types: Chlorophyll a concentration, turbidity, and salinity. We concluded that both zooplankton dispersal through watercourse and species sorting by local factors were important for structuring communities in our study system. Since most studies on dispersal and influence of local factors on zooplankton assemblages in new environment have been done largely in temporal ponds, our findings provide unique insights on how zooplankton communities are jointly regulated by their species dispersal origins and local environmental factors in newly created canals and lakes.