Abstract In general, reservoirs are multi-purpose objects and they often have to fulfil different tasks at the same time. The compliance with these different expectations is more manageable in reservoirs with well-separated heterogeneous basins than in homogenous ones. The Kiskore Reservoir is the second largest standing water in the Carpathian Basin. Its water level is artificially regulated which creates unique habitats with high nature conservation value. Furthermore, the Reservoir is also considered as an important recreation centre in the region. It consists of four basins with different protection degree and management strategy. Here, we tested whether spatial (usage-dependent) or seasonal (time-dependent) segregations characterized the benthic diatom composition in the Reservoir. We also tested the influence of different water usage of basins using diatom metrics and diversity indices. We hypothesized that spatial heterogeneity in diatom composition will be more pronounced than seasonal ones. We also supposed that composition and diversity of diatom assemblages as well as diatom based ecological status will clearly reflect to different management strategies in the basins, whereas we expected moderate ecological status and low diversity in basins with high level of human impact. Our first hypothesis was not confirmed by the results. While diatom composition was clearly heterogeneous in time, surprisingly no usage-dependent segregation was found. Furthermore, our second hypothesis was also only partially confirmed by the results. In early summer, diversity was significantly lower in basins with higher level of human impact, than in the other basins. In late summer, however, diversity was rather directly controlled by nutrients and light not by water usage. Moreover, diatom based ecological status positively correlated to the intensity of recreation activities and negatively to protection degree. Although these results were surprising at the first time, they clearly confirm that a balanced ecological-economical relation can be maintained with properly designed and performed strategies in artificial reservoirs. But protection strategies, because of their exclusive interest to habitat conservation of macroscopic not microscopic organisms, require careful revisions.