Considering the negative effects of wetland degradation, various measures have been implemented to restore wetland habitats for aquatic organisms, and their effectiveness levels must be assessed. To reduce the effects of aquaculture on aquatic communities, pen culture facilities, which are widely distributed in Yangtze-connected lakes, were removed in 2018. We surveyed and compared waterbird communities in Caizi Lake during the four months before (2017–2018) and after net pen removal (2021–2022) to evaluate their effect on the diversity and species composition of wintering waterbirds. After net pen removal, the richness and number of individual waterbird species increased, whereas the Shannon–Wiener diversity index did not change because the increase in the bird number throughout the year was mostly associated with a few species. The response of individual numbers of different guilds to the removal of net pens differed. The number of deep-water fish eaters, seed eaters, and tuber feeders increased, whereas that of invertebrate eaters decreased. The species composition also changed, particularly in the northeastern and southwestern parts of the lake. Differences in waterbird communities between the winters of 2017–2018 and 2021–2022 indicated that net pen removal had a positive impact on waterbird communities.