Horizontal sampling within a lentic oxbow demonstrated the uneven distribution of algae at both large and small scales. An index of heterogeneity is proposed to characterize the fine-scale horizontal patchiness, which is defined as the ratio of the coefficient of variation among samples and the error in counting the algae. Applying a vertical grid sampling strategy, a distinct patchy distribution of several algal species was observed. Most of the patches were formed by those species that have good buoyancy-regulating mechanisms (blue–green algae, dinoflagellates). Atelomixis caused by surface cooling may be the explanation of the heterogeneity. We have shown that the anisotropic horizontal distribution of the phytoplankton could cause high uncertainty in lake quality assessment. Therefore, to improve accuracy composite sampling is needed.