Abstract
Environmental DNA (eDNA) metabarcoding is a powerful technique for assessing biodiversity in threatened Neotropical aquatic environments, yet the effect of water-level fluctuations in lentic systems on eDNA detectability and distribution remains poorly understood. Thus, we conducted a multi-year eDNA metabarcoding survey of the fish community in Ingleses Lake, a small urban Neotropical reservoir, across periods of high and low water levels. We found that eDNA detectability is shaped by hydrology-induced changes, since the mean ɑ-diversity per site was higher and the mean β-diversity was lower during low-water conditions. While fish assemblages maintained a stable core community (PERMANOVA F = 2.26, P = 0.056), a significant difference in the homogeneity of multivariate dispersions was detected (PERMDISP F = 22.23, P = 0.003). These results support the hypothesis that higher water-level conditions of the reservoir led to lower species detectability, probably due to increased eDNA dilution. Critically, combining data from campaigns of both high and low water yielded a near-asymptotic species accumulation curve, demonstrating that temporal replication across dynamic hydrological cycles is crucial for maximising eDNA detection efficiency in Neotropical lentic systems.