Population growth in urban areas changes freshwater ecosystems, and this can have consequences for macrophyte communities as can be seen in the municipalities that border the Capibaribe River, Pernambuco, Brazil. This study reports the effects of urbanization on the composition and structure of macrophyte communities in areas along that river. The following urbanized and non-urbanized sampling sites were chosen: Sites 1 and 2 (municipality of Santa Cruz do Capibaribe), Sites 3 and 4 (municipality of Toritama), and Sites 5 and 6 (metropolitan region of Recife). These sites were visited every two months from January to July 2013 to observe seasonal variation (wet and dry seasons). Thirty-one species were identified. Generally, the non-urbanized sites had a higher number of species. Multivariate analyses indicated significant overall differences between urbanized and non-urbanized areas (R = 0.044; p < 0.001) and between seasons (R = 0.018; p < 0.019). Owing to the large variation in physical, chemical, and biological characteristics between urbanized and non-urbanized areas, we found that urbanization significantly influenced the floristic composition and structure of macrophyte communities.