In this study, we examined the variation of diatom assemblages according to the two sampling times and the four managed basins in Lake Tisza, Hungary. Totally, 235 taxa of benthic diatoms were identified in the 40 samples. Our results highlighted the changes in diatom assemblages based on both taxonomic and trait-based approaches. Although these basins are well-defined with clear objectives, we found that the temporal heterogeneity in diatom composition is more pronounced than the spatial ones. For the biodiversity index, while Shannon diversity is not affected by the water regulation and water management, functional diversity was significantly affected by the intensity of water management. Additionally, we used multimetric index for lakes (MIL) to evaluate the ecological status of Lake Tisza. The results clearly highlighted that while seasonality had a major role in shaping the ecological status, intense recreational activities had no significant effect on water quality: the basin that has the highest level of protection has the lowest ecological status. This suggests that the exclusive interest in habitat conservation and restoration here is macroscopic organisms, not microscopic organisms. Therefore, the protection strategies need to be carefully revised with clearly defined objectives and ultimate goals.