The aim of this study was to reveal the changes of macrophyte community over time and along the course of the Ižica River. In 1996, 2000, and 2016, we surveyed the distribution and abundance of macrophyte species in the lowland Ižica River, which originates in the town of Ig and then flows through an agricultural landscape. We calculated the River Macrophyte Index (RMI), which reflects the ecological status of the river. In 2016, ecomorphological conditions of the river, using the Riparian, Channel and Environmental inventory, were also assessed. In just 10.5 km of the river, we identified 27 taxa of macrophytes, among which Potamogeton natans, Sagittaria sagittifolia, and P. perfoliatus were the most abundant. Detrended correspondence analysis showed that, in 1996, the surveyed stretches differed more according to macrophyte composition than in the following years. The assessed environmental parameters explained 43% of the variability of the macrophyte species; riverbank stability explained 20%, riverbed structure 10%, while vegetation type of the riparian zone and bottom type explained 7 and 5%, respectively. The species composition of the macrophyte community revealed significant changes over the years of the riverine ecosystem. Comparison of RMIs in 1996 revealed better conditions in the upper and middle part of the river, while in 2016, the situation was the opposite, since the conditions in the upper part deteriorated significantly over time, while the lower part of the river had the best ecological status. These changes may be due to a considerable increase in the population of the settlement Ig, while better status in the lower course of the river may be a consequence of improvements in the infrastructure and the use of sustainable agricultural practices in the catchment due to the establishment of a formal area of protection.